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Figure 2 in The complete mitochondrial genome of the leopard shark Triakis semifasciata (Triakidae)

Figure 2. Codon usage in 13 protein-coding genes encoded in the mitochondrial genome of the leopard shark Triakis semifasciata.

Figure 5 in Characterisation of the complete mitochondrial genome of the imperiled Pearl darter Percina aurora (Perciformes: Percidae)

Figure 5. Features present in the Control Region (CR) (987 bp) of the Percina aurora mitogenome. The CR is separated into an extended termination-associated sequence domain (ETAS), a core domain, and a conserved sequence block (CSB) domain. The underlined portion denotes the long tandem repeat sequence within the ETAS domain. The blue-green highlighted sequence represents the ETAS 1 region while the blue highlighted sequence represents the ETAS 2 region. Nucleotides in green, yellow and pink correspond to the F-box, E-box and D-box regions within the central domain, respectively. Nucleotides in cyan, red and dark green correspond to the CSB-1, CSB-2 and CSB-3 regions, respectively.

Figure 5 in The complete mitochondrial genome of the leopard shark Triakis semifasciata (Triakidae)

Figure 5. Phylomitogenomic analysis of the leopard shark Triakis semifasciata and related species in the family Triakidae. Total-evidence phylogenetic tree obtained from a maximum likelihood analysis based on a concatenated alignment of the 13 protein-coding genes (translated) encoded in the mitochondrial genome. Numbers above or below branches are bootstrap support values for the different internal nodes. Photograph of Triakis semifasciata from Matthew Field (used with permisssion).

Figure 3 in The complete mitochondrial genome of the leopard shark Triakis semifasciata (Triakidae)

Figure 3. Selective pressure analysis in the mitochondrial protein-coding genes of the leopard shark Triakis semifasciata. The estimated Ka/Ks ratio for each protein-coding gene is shown.

Figure 4 in Characterisation of the complete mitochondrial genome of the imperiled Pearl darter Percina aurora (Perciformes: Percidae)

Figure 4. Visualisation of the tRNA secondary structure in the mitochondrial genome of Percina aurora.

Figure 2 in Characterisation of the complete mitochondrial genome of the imperiled Pearl darter Percina aurora (Perciformes: Percidae)

Figure 2. Codon usage in 13 protein coding genes of Percina aurora. Columns indicate the relative frequency of synonymous codons separated by amino acid.

Figure 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures

Figure 1. Mitochondrial genome synteny in Cubaris murina and closely related species. A dash (-) before the gene name means that the gene is encoded on the light strand. NCR means a non-coding region that is longer than 100 bp. Cubaris murina is marked in bold black and shades of grey.

Figure 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures

Figure 2. Secondary structure of each transfer RNA (tRNA) visualised in Forna (http://rna.tbi.univie.ac. at/forna).

Table 3 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures

Table 3. Characteristic (AT content, repeat, number of predicted secondary structure, range of ΔG value (kcal/mol)) of control region of Cubaris murina by RNAstructure.<table><tbody><tr><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th>Number of predicted</th><th></th></tr></tbody><tbody><tr><th>Species [reference]</th><td>Name</td><td>Start</td><td>Stop</td><td>(bp)</td><td>Location</td><td>%AT</td><td>Repeat</td><td>secondary structures</td><td>ΔG value (kcal/mol)</td></tr><tr><th>Cubaris murina</th><td>NCR1</td><td>5219</td><td>5360</td><td>142</td><td>Between nad1 and trnN</td><td>52.80%</td><td></td><td>7</td><td>−16.9 to −15.4</td></tr><tr><th>[present study]</th><td>NCR2</td><td>6297</td><td>6666</td><td>370</td><td>Between trnS1 and trnL1</td><td>59.70%</td><td>CT-rich & AT-loop</td><td>20</td><td>−103.7 to −101.0</td></tr><tr><th></th><td>NCR3</td><td>12,550</td><td>12,753</td><td>204</td><td>Between rrnL and trnE</td><td>71.10%</td><td>poly-A</td><td>7</td><td>−17.5 to −17.1</td></tr><tr><th></th><td>NCR4</td><td>12,813</td><td>12,950</td><td>138</td><td>Between trnE and trnV</td><td>71.70%</td><td>AG-rich</td><td>5</td><td>−13.4 to −12.3</td></tr><tr><th>Panulirus argus [Baeza, 2018]</th><td>NCR</td><td>13,525</td><td>14,326</td><td>801</td><td>Between rrnS and trnI</td><td>69.60%</td><td>AT-rich</td><td>7</td><td>−99.20 to −94.52</td></tr><tr><th>Synalpheus microneptunus [Chak et al., 2020]</th><td>NCR</td><td>13,365</td><td>14,198</td><td>834</td><td>Between rrnS and trnI</td><td>79.50%</td><td>AT-rich</td><td>20</td><td>− 104 (lowest)</td></tr></tbody></table>

Complete sequences of six major histocompatibility complex haplotypes rev2

Sequences that the analysis in the paper <a title="Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures" href="https://doi.org/10.1111/tan.15020" target="_blank" rel="noopener">Houwaart et. al. 2023</a> was based on

Table 2 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Table 2. Primers used for PCRs and sequencing (F* forward; R* reverse).<table><tbody><tr><th>Primer</th><th>Sequence</th><th>Reference</th></tr></tbody><tbody><tr><th>MedlinA (F)</th><td>5 ʹ -AACCTGGTTGATCCTGCCAGT-3%</td><td>Medlin et al. (1988)</td></tr><tr><th>MedlinB (R)</th><td>5 ʹ -TGATCCTTCTGCAGGTTCACCTAC-3%</td><td>Medlin et al. (1988)</td></tr><tr><th>SSU-LSU-F (F)</th><td>5 ʹ -TCGCACCTACCGATTGGATG-3%</td><td>This study</td></tr><tr><th>SSU-LSU-R (R)</th><td>5 ʹ -GAAAAGATAACTCTTCCTAG-3%</td><td>This study</td></tr><tr><th>M28S-F (F)</th><td>5 ʹ -TAGCCCTGAAAATGGATGGCGCT-3%</td><td>This study</td></tr><tr><th>28S-4R (R)</th><td>5 ʹ -TTCTGACTTAGAGGCGTTCAG-3%</td><td>Moreira et al. (2007)</td></tr></tbody></table>

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TABLE 1 in Description of the complete larval development of Lysmata amboinensis (De Man) (Decapoda: Lysmatidae) reared under laboratory conditions

TABLE 1. Comparison of selected morphological zoeal stages characters of Lysmata sp. Z—Zoea. Decap.—Decapodite. ZI, ZII, etc.—First zoea, second zoea, etc. Pl—Plumose seta. Si—Simple setae. NA —Not Available. a In ZV it wasn’t yet; b In ZIV it had almost reached it.<table><tbody><tr><th>Morphological feature</th><th>L. amboinensis</th><th>L. amboinensis</th><th>L. ensirostris</th><th>L. vittata</th><th>L. galapagensis</th></tr></tbody><tbody><tr><th></th><td>Present study</td><td>Wunsch 1996</td><td>Bensam&Kartha 1967; Pillai 1974</td><td>Yang&Kim 1999</td><td>Bartilotti et al. 2012</td></tr><tr><th></th><td>10 Z +1 decap.</td><td>11 Z</td><td>9 Z+1 decap.</td><td>9 Z</td><td>7 Z</td></tr><tr><th></th><td>Indian Ocean, Indo-Pacific, South Pacific Ocean, Mozambique Channel</td><td>Indo-Pacific, Red Sea, Atlantic Ocean</td><td>Indo-Pacific</td><td>Indo-Pacific</td><td>E Pacific</td></tr><tr><th>ZI, Total length, mm</th><td>2.8–2.98</td><td>2.70–2.80</td><td>1.89–2.23</td><td>NA</td><td>2.46–2.89</td></tr><tr><th>ZI, carapace length, mm</th><td>0.9–1</td><td>NA</td><td>NA</td><td>0.33–0.37</td><td>0.92–1.00</td></tr><tr><th>ZIV, carapace length, mm</th><td>0.64–1</td><td>NA</td><td>1.01</td><td>0.44</td><td>1.61–2.15</td></tr><tr><th>ZVII, carapace length, mm</th><td>0.84–1.42</td><td>NA</td><td>1.40–1.41</td><td>0.62–0.68</td><td>4.08–4.32</td></tr><tr><th>Last Z, carapace length, mm</th><td>ZX: 2.81–4.35</td><td>ZXI: NA</td><td>ZIX: 3.5</td><td>ZIX: 0.784–0.832</td><td>-</td></tr><tr><th>First Zoea:</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Carapace: Pterigostomian spine</th><td>Present</td><td>Present</td><td>Present</td><td>Present</td><td>Present</td></tr><tr><th>Number of marginal denticles</th><td>3–5</td><td>3–4</td><td>3</td><td>3</td><td>4</td></tr><tr><th>Eyes sessile</th><td>Present</td><td>Present</td><td>Present</td><td>Present</td><td>Present</td></tr><tr><th>Antennule: peduncle and exopod</th><td>Entire</td><td>Entire</td><td>Entire</td><td>Entire</td><td>Entire</td></tr><tr><th>Antennal exopod: 5–6 articles</th><td>11Pl + 1Si</td><td>12Pl + 1Si</td><td>9Pl</td><td>10Pl + 1Si</td><td>11Pl + 1Si</td></tr><tr><th>Pair of dorsal spines on 5th pleomere</th><td>Present</td><td>Present</td><td>Present</td><td>Present</td><td>Present</td></tr><tr><th>Pleopods</th><td>Absent</td><td>Absent</td><td>Absent</td><td>Absent</td><td>Absent</td></tr><tr><th>Uropods</th><td>Absent</td><td>Absent</td><td>Absent</td><td>Absent</td><td>Absent</td></tr><tr><th>Older Zoeas:</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Eyes stalked and pedunculate</th><td>ZII</td><td>ZII</td><td>ZII</td><td>ZII</td><td>ZII</td></tr><tr><th>Carapace without marginal denticles</th><td>ZVII</td><td>ZVII</td><td>ZV</td><td>ZIX</td><td>ZV</td></tr><tr><th>Carapace with cervical carinae</th><td>Absent</td><td>Absent</td><td>Absent</td><td>Absent</td><td>Absent</td></tr><tr><th>Rostrum first dorsal spine</th><td>ZVII</td><td>ZVI</td><td>ZIV</td><td>ZIII</td><td>ZII</td></tr><tr><th>Antennal exopod entire</th><td>ZIV</td><td>ZIV</td><td>ZV</td><td>ZIV</td><td>ZIV</td></tr><tr><th>First pereiopod:</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Biramous bud</th><td>ZII (small bud: ZI)</td><td>ZII</td><td>ZII</td><td>ZII</td><td>ZI</td></tr><tr><th></th><td>Present study</td><td>Wunsch 1996</td><td>Bensam&Kartha 1967; Pillai 1974</td><td>Yang&Kim 1999</td><td>Bartilotti et al. 2012</td></tr><tr><th></th><td>10 Z +1 decap.</td><td>11 Z</td><td>9 Z+1 decap.</td><td>9 Z</td><td>7 Z</td></tr><tr><th></th><td>Indian Ocean, Indo-Pacific, South Pacific Ocean, Mozambique Channel</td><td>Indo-Pacific, Red Sea, Atlantic Ocean</td><td>Indo-Pacific</td><td>Indo-Pacific</td><td>E Pacific</td></tr><tr><th>Functional</th><td>ZIII</td><td>ZIII</td><td>ZIII</td><td>ZIII</td><td>ZII</td></tr><tr><th>Second pereiopod:</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Biramous bud</th><td>ZIV</td><td>ZIV</td><td>ZIII</td><td>ZIII</td><td>ZIII</td></tr><tr><th>Functional</th><td>ZV</td><td>ZV</td><td>ZIV</td><td>ZV</td><td>ZIV</td></tr><tr><th>Third pereiopod:</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Biramous bud</th><td>ZV</td><td>ZV</td><td>ZIV</td><td>ZIV (unir. rud)</td><td>ZV</td></tr><tr><th>Functional</th><td>ZVI</td><td>ZVI</td><td>ZV</td><td>ZVII</td><td>ZVI</td></tr><tr><th>Fourth pereiopod:</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Biramous bud</th><td>ZVI</td><td>ZVI</td><td>ZV</td><td>ZIV (unir. rud)</td><td>ZV</td></tr><tr><th>Functional</th><td>ZVII</td><td>ZVII</td><td>ZVI</td><td>ZVIII</td><td>ZVI</td></tr><tr><th>Fifth pereiopod:</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Uniramous bud</th><td>ZIII (small bud: ZII)</td><td>ZIII</td><td>ZIII</td><td>ZIII</td><td>ZI</td></tr><tr><th>Functional</th><td>ZIV</td><td>ZIV</td><td>ZIV</td><td>ZV</td><td>ZII</td></tr><tr><th>Pereiopods with paddled-like propodus</th><td>3 rd, 4 th and 5 th</td><td>3 rd, 4 th and 5 th</td><td>5th</td><td>5th</td><td>5th</td></tr><tr><th>5th pleomere without dorso-lat spines</th><td>ZVIII</td><td>ZIII</td><td>NA</td><td>ZV</td><td>NA</td></tr><tr><th>3rd pleomere with curved spine</th><td>Absent</td><td>Absent</td><td>Absent</td><td>Absent</td><td>Present</td></tr><tr><th>Pleopods:</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Small buds</th><td>ZVIII</td><td>NA</td><td>-</td><td>ZV</td><td>ZVI</td></tr><tr><th>Biramous buds</th><td>ZIX</td><td>ZIX (day 40)</td><td>ZVII</td><td>ZVII</td><td>-</td></tr><tr><th>Differentiated protopod</th><td>ZX</td><td>ZX (day 80)</td><td>ZVIII</td><td>ZIX</td><td>ZVII</td></tr><tr><th>With appendix interna</th><td>-</td><td>ZXI (day 120)</td><td>ZIX</td><td>-</td><td>NA</td></tr><tr><th>Telson margins laterally parallel</th><td>ZV</td><td>ZV</td><td>ZV</td><td>ZVII</td><td>ZV</td></tr></tbody></table>......continued on the next pageTABLE 1. (Continued)......continued on the next page

Table 1 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Table 1. Opalinid species investigated in the present study. All localities are from China. Morphological identification of each species was carried out in the articles indicated in the ‘reference’ column.<table><tbody><tr><th>Species</th><th>Host</th><th>Prevalence</th><th>Locality</th><th>Reference</th></tr></tbody><tbody><tr><th>Opalina undulata Nie* 1935</th><td>Fejervarya limnocharis (Gravenhorst* 1829) Iskandar* 1998</td><td>7.7% (22/285)</td><td>Diaocha Lake* Hubei Province</td><td>Li et al. (2018)</td></tr><tr><th>Opalina triangulata Metcalf* 1923</th><td>F. limnocharis</td><td>21.5% (9/42)</td><td>Diaocha Lake* Hubei Province</td><td>Wang et al. (2019)</td></tr><tr><th>Opalina japonica Sugiyama* 1920</th><td>Rana chensinensis David * 1875</td><td>33.3% (4/12)</td><td>Xinbin County* Liaoning Province</td><td>Unpublished</td></tr><tr><th>Opalina obtrigonoidea Metcalf* 1923</th><td>Duttaphrynus melanostictus (Schneider* 1799) Frost et al. * 2006</td><td>31.4% (11/35)</td><td>Yubei City* Chongquin Province</td><td>Zhao et al. (2020)</td></tr><tr><th>Opalina longa Bezzenberger* 1904 (= Cepedea longa)a</th><td>F. limnocharis</td><td>35.8% (76/ 212)</td><td>Honghu Lake* Hubei Province</td><td>Li et al. (2017a)</td></tr><tr><th>Protoopalina limnocharis Nie * 1932</th><td>F. limnocharis</td><td>25.6% (32/125)</td><td>Meishan County* Sichuan Province</td><td>Zou et al. (2018)</td></tr><tr><th>Protoopalina pingi Nie* 1935</th><td>Pelophylax nigromaculatus (Hallowell* 1861) Fei et al. * 2005</td><td>40.4% (42/104)</td><td>Honghu Lake* Hubei Province</td><td>Li et al. (2014)</td></tr><tr><th>Zelleriella orientalis Nie* 1935</th><td>Microhyla ornate (Duméril & Bibron* 1841) Boulenger* 1882</td><td>16.2% (6/37)</td><td>Nanning City* Guangxi Province</td><td>Unpublished</td></tr><tr><th>Zelleriella sp.</th><td>Hyla chinensis Gunther * 1858</td><td>11.1% (2/18)</td><td>Sanming City* Fujian Province</td><td>Unpublished</td></tr></tbody></table>aThe initial identification of this species as Cepedea longa followed the proposal by Metcalf (1923). See Discussion section for the justification of the change.

Table 3 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Table 3. List of sequences used in the present study. Sequences lacking>100 bases at the 5 ʹ or 3 ʹ ends are shown in parentheses. New sequences are marked in bold.<table><tbody><tr><th>Sequence/species</th><th>Accession sequence</th></tr><tr><th>Number</th><th>Length</th><th>GC%</th><th>Source</th></tr><tr><th>SSU rDNA</th></tr><tr><th>STRAMENOPILES</th></tr><tr><th>OPALINATA</th></tr><tr><th>Opalinida</th></tr><tr><th>(Protoopalina intestinalis (Stein* 1856) Metcalf* 1923)</th></tr></tbody><tbody><tr><th></th><td>AY576545</td><td>1409</td><td>33.6</td><td>Kostka et al. (2004)</td></tr><tr><th>(Protoopalina axonucleata Metcalf * 1923a)</th><td>AB175929</td><td>1263</td><td>32.5</td><td>Nishi et al. (2005)</td></tr><tr><th>Protoopalina limnocharis</th><td>MN625264</td><td>1829</td><td>32.2</td><td>This study</td></tr><tr><th>Protoopalina pingi</th><td>MN625266</td><td>1830</td><td>32.4</td><td>This study</td></tr><tr><th>Zelleriella orientalis</th><td>MN625263</td><td>2143</td><td>26.4</td><td>This study</td></tr><tr><th>Zelleriella sp.</th><td>MN625265</td><td>2143</td><td>26.4</td><td>This study</td></tr><tr><th>Opalina undulata</th><td>MF434114</td><td>2167</td><td>26.8</td><td>Li et al. (2018)</td></tr><tr><th>Opalina triangulata</th><td>MK872804</td><td>2166</td><td>26.8</td><td>Wang et al. (2019)</td></tr><tr><th>Opalina obtrigonoidea</th><td>MK970648</td><td>2167</td><td>26.8</td><td>Zhao et al. (2020)</td></tr><tr><th>Opalina japonica</th><td>MN625267</td><td>2170</td><td>26.0</td><td>This study</td></tr><tr><th>Opalina longa</th><td>MN625268</td><td>2171</td><td>27.7</td><td>This study</td></tr><tr><th>Proteromonadida</th></tr><tr><th>Karotomorpha sp.</th><td>DQ431242</td><td>1858</td><td>44.1</td><td>Kostka et al. (2007)</td></tr><tr><th>(Karotomorpha sp.)</th><td>DQ431243</td><td>1424</td><td>46.2</td><td>Kostka et al. (2007)</td></tr><tr><th>Proteromonas lacertae Grassé * 1879</th><td>U37108</td><td>1743</td><td>37.4</td><td>Leipe et al. (1996)</td></tr><tr><th>BLASTOCYSTIDA</th></tr><tr><th>Blastocystis cycluri Singh et al. * 1996</th><td>AY266474</td><td>1848</td><td>35.6</td><td>Yoshikawa et al. (2004)</td></tr><tr><th>Blastocystis lapemi Teow et al. * 1991 Blastocystis pythoni Singh et al. * 1996</th><td>AY266471 AY266472</td><td>1840 1794</td><td>36.7 39.1</td><td>Yoshikawa et al. (2004) Yoshikawa et al. (2004)</td></tr><tr><th>Blastocystis hominis (Swaine & Britain* 1849) Brumpt* 1912</th><td></td><td></td><td></td></tr><tr><th>Blastocystis ratti Chen et al. * 1997 PLACIDIDA</th><td>AB023499 AY590114</td><td>1740 1730</td><td>43.6 40.3</td><td>Arisue et al. (2002) Noel et al. (2005)</td></tr><tr><th>Placidia cafeteriopsis Moriya et al. * 2002</th><td>JF834161</td><td>1775</td><td>49.4</td><td>Chan YF* Chen CW* Tsai AY* Chiang KP* unpublished</td></tr><tr><th>Suigetsumonas clinomigrationis Okamura & Kondo * 2015</th><td></td><td></td><td></td></tr><tr><th>Wobblia lunata Moriya et al. * 2000 BICOSOECIDA</th><td>AB976561 AB032606</td><td>1769 1726</td><td>52.0 49.1</td><td>Okamura and Kondo (2015) Moriya et al. (2000)</td></tr><tr><th>Bicosoeca petiolata (Stein* 1878) Prinsheim* 1946</th><td></td><td></td><td></td></tr><tr><th></th><td>AY520444</td><td>1809</td><td>48.6</td><td>Cavalier-Smith and Chao (2006)</td></tr><tr><th>Cafeteria roenbergensis Fenchel & Patterson * 1988</th><td></td><td></td><td></td></tr><tr><th></th><td>AF174364</td><td>1695</td><td>47.1</td><td>Atkins et al. (2000)</td></tr><tr><th>ALVEOLATA</th></tr><tr><th>APICOMPLEXA</th></tr><tr><th>Babesia gibsoni (Patton* 1910)</th><td>KC461261</td><td>1665</td><td>45.5</td><td>Mandal et al. (2015)</td></tr><tr><th>Eimeria necatrix Johnson * 1930</th><td>KT184349</td><td>1763</td><td>46.8</td><td>Ogedengbe et al. (2016)</td></tr><tr><th>DINOFLAGELLATA</th></tr><tr><th>Blastodinium contortum Chatton * 1908</th><td>DQ317537</td><td>1799</td><td>44.8</td><td>Skovgaard et al. (2007)</td></tr><tr><th>Prorocentrum arenarium Faust * 1994</th><td>Y16234</td><td>1788</td><td>46.4</td><td>Grzebyk et al. (1998)</td></tr><tr><th>CILIOPHORA</th></tr><tr><th>LItonotus paracygnus Song* 1994</th><td>EU242509</td><td>1635</td><td>42.0</td><td>Gao et al. (2008)</td></tr><tr><th>Paramecium buestchlii van As et al. * 1998</th><td>KM091234</td><td>1703</td><td>44.2</td><td>Krenek et al. (2015)</td></tr><tr><th>AMORPHEA</th></tr><tr><th>CHOANOZOA</th></tr><tr><th>Salpingoeca infusionum Kent * 1880</th><td>AF100941</td><td>1978</td><td>49.6</td><td>Collins (1998)</td></tr><tr><th>ITS region (OPALINATA)</th><td></td><td></td><td></td><td></td></tr><tr><th>Protoopalina limnocharis</th><td>MN630239</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>231</td><td>2.2</td><td></td></tr><tr><th>5.8S</th><td></td><td>154</td><td>35.7</td><td></td></tr><tr><th>ITS2</th><td></td><td>229</td><td>4.4</td><td></td></tr><tr><th>Protoopalina pingi</th><td>MN630241</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>237</td><td>2.1</td><td></td></tr><tr><th>5.8S</th><td></td><td>154</td><td>36.4</td><td></td></tr><tr><th>ITS2</th><td></td><td>218</td><td>4.6</td><td></td></tr><tr><th>Zelleriella orientalis</th><td>MN630236</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>291</td><td>2.8</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>26.4</td><td></td></tr><tr><th>ITS2</th><td></td><td>285</td><td>2.5</td><td></td></tr><tr><th>Zelleriella sp.</th><td>MN630237</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>290</td><td>2.8</td><td></td></tr><tr><th>5.8S</th><td></td><td>166</td><td>26.5</td><td></td></tr><tr><th>ITS2</th><td></td><td>279</td><td>2.5</td><td></td></tr><tr><th>Opalina undulata</th><td>MG816209</td><td></td><td></td><td>Li et al. (2018)</td></tr><tr><th>ITS1</th><td></td><td>325</td><td>1.5</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.0</td><td></td></tr><tr><th>ITS2</th><td></td><td>290</td><td>2.4</td><td></td></tr><tr><th>Opalina triangulata</th><td>MK872803</td><td></td><td></td><td>Wang et al. (2019)</td></tr><tr><th>ITS1</th><td></td><td>292</td><td>1.7</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>284</td><td>1.8</td><td></td></tr><tr><th>Opalina obtrigonoidea</th><td>MK973090</td><td></td><td></td><td>Zhao et al. (2020)</td></tr><tr><th>ITS1</th><td></td><td>323</td><td>1.6</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>287</td><td>1.7</td><td></td></tr><tr><th>Opalina japonica</th><td>MN630238</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>357</td><td>1.7</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>358</td><td>2.5</td><td></td></tr><tr><th>Opalina longa</th><td>MN630240</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>283</td><td>1.8</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>261</td><td>2.3</td><td></td></tr><tr><th>LSU rDNA (OPALINATA)</th><td></td><td></td><td></td><td></td></tr><tr><th>Protoopalina limnocharis</th><td>MN638759</td><td>3652</td><td>26.7</td><td>This study</td></tr><tr><th>Protoopalina pingi</th><td>MN638761</td><td>3647</td><td>26.9</td><td>This study</td></tr><tr><th>Zelleriella orientalis</th><td>MN638760</td><td>4064</td><td>23.0</td><td>This study</td></tr><tr><th>Zelleriella sp.</th><td>MN638763</td><td>4102</td><td>22.8</td><td>This study</td></tr><tr><th>Opalina undulata</th><td>MN638758</td><td>4108</td><td>22.8</td><td>This study</td></tr><tr><th>Opalina triangulata</th><td>MN638762</td><td>4043</td><td>23.9</td><td>This study</td></tr><tr><th>Opalina obtrigonoidea</th><td>MW504710</td><td>4122</td><td>22.5</td><td>This study</td></tr><tr><th>Opalina japonica</th><td>MN638764</td><td>4120</td><td>22.4</td><td>This study</td></tr><tr><th>Opalina longa</th><td>MN638765</td><td>4096</td><td>23.6</td><td>This study</td></tr></tbody></table>aNishi et al. (2005: 701–702) indicated that ‘the four sequences from Protoopalina sp. were all identical* although they were isolated at different geographical locations.Futhermore* the genus Protoopalina is presently restricted to the host species Rana nigromaculata in Japan.They commonly retain four relatively large nuclei* show similar morphological characters (Table 1)* and are classified as P.japonica (Hara 1934) ’. However* the work by Hara (1934) is on the cell morphology and microtubular structures of Protoopalina axonucleata * and he did not mention any other species in his work.According to the statements by Nishi et al. (2005) * their isolates corresponded to the same species studied by Hara (1934) and should be identified as P.axonucleata. The name Protoopalina japonica is a nomen nudum because this species has never been described.

Table 7 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Table 7. List of nomenclatural acts.<table><tbody><tr><th>Taxon nameb</th><th>Previous name</th><th>Comments</th></tr><tr><th>Opalina Purkinje & Valentin * 1835 (= Cepedea Metcalf * 1920)</th></tr></tbody><tbody><tr><th>Opalina acuta (Delvinquier* Markus & Passmore* 1993) comb. nov.</th><td>Cepedea acuta Delvinquier * Markus & Passmore* 1992</td><td></td></tr><tr><th>Opalina affinis Nazaretskaja * 1922</th><td>Cepedea affinis (Nazaretskaja* 1922) Walton* 1964</td><td></td></tr><tr><th>Opalina africana (Tuzet & Zuber-Vogeli* 1954) comb. nov.</th><td>Cepedea africana Tuzet & Zuber-Vogeli * 1954</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina amygdala (Boisson* 1965) Delvinquier et al. * 1991</th><td>Cepedea amygdala Boisson * 1965</td><td>Proposed as synonym of Opalina foliacea by Affa’a and Lynn (1994)</td></tr><tr><th>Opalina baudinii (Metcalf* 1923) comb. nov.</th><td>Cepedea baudini Metcalf * 1923</td><td></td></tr><tr><th>Opalina boissoni (Tuzet & Knoepffler* 1968) comb. nov.</th><td>Cepedea boissoni Tuzet & Knoepffler * 1968</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina borneonensis (Metcalf* 1923) comb. nov.</th><td>Cepedea borneonensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina buergeri (Metcalf* 1923) comb. nov.</th><td>Cepedea buergeri Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina brumpti (Cordero* 1928) comb. nov.</th><td>Cepedea brumpti Cordero * 1928</td><td></td></tr><tr><th>Opalina cantabrigensis (Metcalf* 1923)</th><td>Cepedea cantabrigensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina celebensis (Metcalf* 1923) comb. nov.</th><td>Cepedea celebensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina ciliata (Metcalf* 1940) comb. nov.</th><td>Cepedea ciliata Metcalf * 1940</td><td></td></tr><tr><th>Opalina crispata (Boisson* 1965) comb. nov.</th><td>Cepedea crispata Boisson * 1965</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina daloalensis (Tuzet & Zuber-Vogeli* 1954) comb. nov.</th><td>Cepedea daloalensis Tuzet & Zuber-Vogeli * 1954</td><td></td></tr><tr><th>Opalina dimidiata Stein * 1860</th><td>Cepedea dimidiata (Stein* 1860) Metcalf* 1923</td><td></td></tr><tr><th>Opalina dolichosoma (Metcalf* 1923) comb. nov.</th><td>Cepedea dolichosoma Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina dracuncula (Boisson* 1957) comb. nov.</th><td>Cepedea dracuncula Boisson * 1957</td><td></td></tr><tr><th>Opalina elongata Gourvitsch * 1926</th><td>Cepedea elongata (Gourvitsch* 1926) Banina* 1962</td><td></td></tr><tr><th>Opalina flava Stokes * 1884</th><td>Cepedea flava (Stokes* 1884) Metcalf* 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina floridensis (Metcalf* 1923) comb. nov.</th><td>Cepedea floridensis Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina foliacea (Boisson* 1959) Delvinquier et al. * 1991</th><td>Cepedea foliacea Boisson * 1959</td><td></td></tr><tr><th>Opalina formosae (Metcalf* 1923) comb. nov.</th><td>Cepedea formosae Metcalf * 1923</td><td></td></tr><tr><th>Opalina fujiensis (Metcalf* 1923) comb. nov.</th><td>Cepedea fujiensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina fusiformis (Tuzet & Knoepffler* 1968) comb. nov.</th><td>Cepedea fusiformis Tuzet & Knoepfler * 1968</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina globosa (Metcalf* 1923) comb. nov.</th><td>Cepedea globosa Metcalf * 1923</td><td></td></tr><tr><th>Opalina gracilis (Banina* 1952) comb. nov.</th><td>Cepedea gracilis Banina * 1952</td><td></td></tr><tr><th>Opalina hasseltii (Metcalf* 1940) comb. nov.</th><td>Cepedea hasseltii Metcalf * 1940</td><td></td></tr><tr><th>Opalina hispanica (Metcalf* 1923) comb. nov.</th><td>Cepedea hispanica Metcalf * 1923</td><td>Proposed as synonym of Opalina longa by Metcalf (1940)</td></tr><tr><th>Opalina hosei (Metcalf* 1940) comb. nov.</th><td>Cepedea hosei Metcalf * 1940</td><td></td></tr><tr><th>Opalina hylae (Khan* 1962) comb. nov.</th><td>Cepedea hylae Khan * 1962</td><td></td></tr><tr><th>Opalina lemuriae (Metcalf* 1940) comb. nov.</th><td>Cepedea lemuriae Metcalf * 1940</td><td></td></tr><tr><th>Opalina longa Bezzenberger * 1904</th><td>Cepdea longa (Bezzenberger* 1904) Metcalf* 1923</td><td></td></tr><tr><th>Opalina luzonensis (Metcalf* 1940) comb. nov.</th><td>Cepedea luzonensis Metcalf * 1940</td><td></td></tr><tr><th>Opalina macronucleata (Banina* 1952) comb. nov.</th><td>Cepedea macronucleata Banina * 1952</td><td></td></tr><tr><th>Opalina madagascariensis (Metcalf* 1923) comb. nov.</th><td>Cepedea madagascariensis Metcalf * 1923</td><td>Considered in part as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina magna (Metcalf* 1923) comb. nov.</th><td>Cepedea magna Metcalf * 1923</td><td>(= Opalina sudafricana Fantham * 1923) (following Delvinquier et al. 1993)</td></tr><tr><th>Opalina marginata (Amaro* 1964) comb. nov.</th><td>Cepedea marginata Amaro * 1964</td><td></td></tr><tr><th>Opalina metcalfi (Bhatia & Gulati* 1927) comb. nov.</th><td>Cepedea metcalfi Bhatia & Gulati * 1927</td><td></td></tr><tr><th>Opalina mexicana (Metcalf* 1923) comb. nov.</th><td>Cepedea mexicana Metcalf * 1923</td><td></td></tr><tr><th>Opalina microhylae (Metcalf* 1940) comb. nov.</th><td>Cepedea microhylae Metcalf * 1940</td><td></td></tr><tr><th>Opalina minor (Metcalf* 1923) comb. nov.</th><td>Cepedea minor Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina mogyana Carini * 1937</th><td>Cepedea mogyana (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th>Opalina multiformis (Metcalf* 1923) comb. nov.</th><td>Cepedea multiformis Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina obovoidea (Metcalf* 1923) comb. nov.</th><td>Cepedea obovoidea Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina obtrigonoidea Metcalf * 1923</th><td>Cepedea obtrigonoidea (Metcalf* 1923) Affa’a & Lynn* 1994</td><td></td></tr><tr><th>Opalina occidentalis (Metcalf* 1923) comb. nov.</th><td>Cepedea occidentalis Metcalf * 1923</td><td></td></tr><tr><th>Opalina ophis (Metcalf* 1923) comb. nov.</th><td>Cepedea ophis Metcalf * 1923</td><td></td></tr><tr><th>Opalina parva (Lu* 1945) comb. nov.</th><td>Cepedea parva Lu * 1945</td><td></td></tr><tr><th>Opalina philauti (Uttangi* 1952) comb. nov.</th><td>Cepedea philauti Uttangi * 1952</td><td></td></tr><tr><th>Opalina philippensis (Metcalf* 1940) comb. nov.</th><td>Cepedea philippensis Metcalf * 1940</td><td></td></tr><tr><th>Opalina phrynomantidis (Metcalf* 1923) comb. nov.</th><td>Cepedea phrynomantidis Metcalf * 1923</td><td>Proposed as synonym of Opalina magna by Delvinquier et al. (1993)</td></tr><tr><th>Opalina plata (Metcalf* 1940) comb. nov.</th><td>Cepedea plata Metcalf * 1940</td><td></td></tr><tr><th>Opalina pulchra (Metcalf* 1923) comb. nov.</th><td>Cepedea pulchra Metcalf * 1923</td><td></td></tr><tr><th>Opalina punjagbensis (Bhatia & Gulati* 1927) comb. nov.</th><td>Cepedea punjagbensis Bhatia & Gulati * 1927</td><td></td></tr><tr><th>Opalina rubra Carini * 1937</th><td>Cepedea rubra (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th>Opalina rugosa Carini * 1937</th><td>Cepedea rugosa (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th>Opalina saharana (Metcalf* 1923) comb. nov.</th><td>Cepedea saharana Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina scalpriformis Ghosh * 1918</th><td>Cepedea scalpriformis (Ghosh* 1918) Metcalf* 1940</td><td></td></tr><tr><th>Opalina segmentata (Metcalf* 1923) comb. nov.</th><td>Cepedea segmentata Metcalf * 1923</td><td></td></tr><tr><th>Opalina seychellensis (Metcalf* 1923) comb. nov.</th><td>Cepedea seychellensis Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina sialkoti (Bathia & Gulati* 1927) comb. nov.</th><td>Cepedea sialkoti Bathia & Gulati * 1927</td><td></td></tr><tr><th>Opalina siamensis (Metcalf* 1940) comb. nov.</th><td>Cepedea siamensis Metcalf * 1940</td><td></td></tr><tr><th>Opalina spinifera (Metcalf* 1923) comb. nov.</th><td>Cepedea spinifera Metcalf * 1923</td><td></td></tr><tr><th>Opalina subcylindrica (Mello* 1932) comb. nov.</th><td>Cepedea subcylindrica Mello * 1932</td><td></td></tr><tr><th>Opalina sudafricana Fantham * 1923</th><td>Cepedea sudafricana (Fantam* 1923) Affa’a & Lynn* 1994</td><td></td></tr><tr><th>Opalina thiagi (Mello* 1931) comb. nov.</th><td>Cepedea thiagi Mello * 1931</td><td></td></tr><tr><th>Opalina vanniekerkae (Delvinquier* Markus & Passmore* 1993)</th><td>Cepedea vanniekerkae Delvinquier * Markus & Passmore* 1993</td><td></td></tr><tr><th>Opalina virgula Dobell * 1910</th><td>Cepedea virgula (Dobell* 1910) Metcalf* 1940</td><td></td></tr><tr><th>Opalina virguloidea Metcalf * 1923</th><td>Cepedea virguloidea (Metcalf* 1923) Affa’a & Lynn* 1994</td><td></td></tr><tr><th>Protoopalina Metcalf * 1918 (= Bezzenbergeria Earl * 1973)</th><td></td><td></td></tr><tr><th>Protoopalina lanceolata Bezzenberger* 1904</th><td>Bezzenbergeria lanceolata [(Bezzenberger* 1904) Metcalf* 1923] Earl* 1973 Cepedea lanceolata (Bezzenberger* 1904) Metcalf* 1923</td><td></td></tr><tr><th>Protoopalina axoucleata Metcalf * 1923</th><td>Protoopalina japonica Nishi et al. * 2005</td><td>Nomem nudum</td></tr></tbody></table>aThe species Cepedea lanceolatum was listed by Delvinquier and Patterson (1993)* citing Evans et al. (1977) * but without specifying the author and publication year.We have been unable to obtain a copy of the paper by Evans et al. (1977) in order to search for a description or the reference to the original source.Therefore* we have not included this species in the list.If it were to be included* the correct species name would be Opalina lanceolata.bEarl (1973) proposed the suppression of 88 species/subspecies of Opalinida because he deemed them inadequately described:certain characteristics were absent from the original descriptions (such as the length of the falx)* and the descriptions were based on type specimens rather than on populations.

opencc-by-4.0Aug 2024View details →

COCONUT 2.0 - Complete database

<h1>COCONUT Release Notes:</h1> <ul> <li>Updated IUPAC Names - OpenEye Lexichem</li> <li>Generated NP Classifier types - https://npclassifier.ucsd.edu</li> </ul> <h1>COCONUT (Collection of Open Natural Products) Online</h1> <a href="https://coconut.naturalproducts.net/" target="_blank" rel="noopener noreferrer">COlleCtion of Open NatUral producTs (COCONUT)</a> is an aggregated dataset comprising elucidated and predicted natural products (NPs) from open repositories. It offers a user-friendly web interface for browsing, searching, and efficiently downloading NPs. The latest database integrates more than 63 open NP resources, providing unrestricted access to data free of charge. Each entry in the database represents a "flat" NP structure, accompanied by information on its known stereochemical forms, relevant literature, producing organisms, natural geographical distribution, and <a href="https://api.naturalproducts.net/docs" target="_blank" rel="noopener noreferrer">precomputed</a> molecular properties. <h3>Summary of the COCONUT database's statistics:</h3> <table> <tbody> <tr> <th>Total Molecules</th> <th>Total Collections</th> <th>Unique Organisms</th> <th>Citations Mapped</th> </tr> </tbody> <tbody> <tr> <td>695,133</td> <td>63</td> <td>53,092</td> <td> 34,991 </td> </tr> </tbody> </table>   <h3>COCONUT was meticulously assembled from a range of public databases and primary sources, including:</h3> <table> <tbody> <tr> <th>S.No</th> <th>Database name</th> <th>Entries integrated in COCONUT</th> <th>Latest resource URL</th> </tr> </tbody> <tbody> <tr> <td>1</td> <td>AfroCancer</td> <td>390</td> <td>Fidele Ntie-Kang, Justina Ngozi Nwodo, Akachukwu Ibezim, Conrad Veranso Simoben, Berin Karaman, Valery Fuh Ngwa, Wolfgang Sippl, Michael Umale Adikwu, and Luc Meva’a Mbaze Journal of Chemical Information and Modeling 2014 54 (9), 2433-2450 <a href="https://doi.org/10.1021/ci5003697" target="_blank" rel="noopener noreferrer">https://doi.org/10.1021/ci5003697</a></td> </tr> <tr> <td>2</td> <td>AfroDB</td> <td>953</td> <td>Fidele Ntie-Kang ,Denis Zofou,Smith B. Babiaka,Rolande Meudom,Michael Scharfe,Lydia L. Lifongo,James A. Mbah,Luc Meva’a Mbaze,Wolfgang Sippl,Simon M. N. Efange <a href="https://doi.org/10.1371/journal.pone.0078085" target="_blank" rel="noopener noreferrer">https://doi.org/10.1371/journal.pone.0078085</a></td> </tr> <tr> <td>3</td> <td>AfroMalariaDB</td> <td>265</td> <td>Onguéné, P.A., Ntie-Kang, F., Mbah, J.A. et al. The potential of anti-malarial compounds derived from African medicinal plants, part III: an in silico evaluation of drug metabolism and pharmacokinetics profiling. Org Med Chem Lett 4, 6 (2014). <a href="https://doi.org/10.1186/s13588-014-0006-x" target="_blank" rel="noopener noreferrer">https://doi.org/10.1186/s13588-014-0006-x</a></td> </tr> <tr> <td>4</td> <td>AnalytiCon Discovery NPs</td> <td>5,147</td> <td>Natural products are a sebset of AnalytiCon Discovery NPs <a href="https://ac-discovery.com/screening-libraries/" target="_blank" rel="noopener noreferrer">https://ac-discovery.com/screening-libraries/</a></td> </tr> <tr> <td>5</td> <td>BIOFACQUIM</td> <td>605</td> <td>Pilón-Jiménez, B.A.; Saldívar-González, F.I.; Díaz-Eufracio, B.I.; Medina-Franco, J.L. BIOFACQUIM: A Mexican Compound Database of Natural Products. Biomolecules 2019, 9, 31. <a href="https://doi.org/10.3390/biom9010031" target="_blank" rel="noopener noreferrer">https://doi.org/10.3390/biom9010031</a></td> </tr> <tr> <td>6</td> <td>BitterDB</td> <td>685</td> <td>Ayana Dagan-Wiener, Antonella Di Pizio, Ido Nissim, Malkeet S Bahia, Nitzan Dubovski, Eitan Margulis, Masha Y Niv, BitterDB: taste ligands and receptors database in 2019, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D1179–D1185, <a href="https://doi.org/10.1093/nar/gky974" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gky974</a></td> </tr> <tr> <td>7</td> <td>Carotenoids Database</td> <td>1,195</td> <td>Junko Yabuzaki, Carotenoids Database: structures, chemical fingerprints and distribution among organisms, Database, Volume 2017, 2017, bax004, <a href="https://doi.org/10.1093/database/bax004" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/database/bax004</a></td> </tr> <tr> <td>8</td> <td>ChEBI NPs</td> <td>16,215</td> <td>Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Bhavana Harsha, Namrata Kale, Venkatesh Muthukrishnan, Gareth Owen, Steve Turner, Mark Williams, Christoph Steinbeck, The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013, Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D456–D463, <a href="https://doi.org/10.1093/nar/gks1146" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gks1146</a></td> </tr> <tr> <td>9</td> <td>ChEMBL NPs</td> <td>1,910</td> <td>Anna Gaulton, Anne Hersey, Michał Nowotka, A. Patrícia Bento, Jon Chambers, David Mendez, Prudence Mutowo, Francis Atkinson, Louisa J. Bellis, Elena Cibrián-Uhalte, Mark Davies, Nathan Dedman, Anneli Karlsson, María Paula Magariños, John P. Overington, George Papadatos, Ines Smit, Andrew R. Leach, The ChEMBL database in 2017, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D945–D954, <a href="https://doi.org/10.1093/nar/gkw1074" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gkw1074</a></td> </tr> <tr> <td>10</td> <td>ChemSpider NPs</td> <td>9,740</td> <td>Harry E. Pence and Antony Williams Journal of Chemical Education 2010 87 (11), 1123-1124 <a href="https://doi.org/10.1021/ed100697w" target="_blank" rel="noopener noreferrer">https://doi.org/10.1021/ed100697w</a></td> </tr> <tr> <td>11</td> <td>CMAUP (cCollective molecular activities of useful plants)</td> <td>47,593</td> <td>Xian Zeng, Peng Zhang, Yali Wang, Chu Qin, Shangying Chen, Weidong He, Lin Tao, Ying Tan, Dan Gao, Bohua Wang, Zhe Chen, Weiping Chen, Yu Yang Jiang, Yu Zong Chen, CMAUP: a database of collective molecular activities of useful plants, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D1118–D1127, <a href="https://doi.org/10.1093/nar/gky965" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gky965</a></td> </tr> <tr> <td>12</td> <td>ConMedNP</td> <td>3,111</td> <td>DOI <a href="https://doi.org/10.1039/C3RA43754J" target="_blank" rel="noopener noreferrer">https://doi.org/10.1039/C3RA43754J</a></td> </tr> <tr> <td>13</td> <td>ETM (Ethiopian Traditional Medicine) DB</td> <td>1,798</td> <td>Bultum, L.E., Woyessa, A.M. & Lee, D. ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database. BMC Complement Altern Med 19, 212 (2019). <a href="https://doi.org/10.1186/s12906-019-2634-1" target="_blank" rel="noopener noreferrer">https://doi.org/10.1186/s12906-019-2634-1</a></td> </tr> <tr> <td>14</td> <td>Exposome-explorer</td> <td>434</td> <td>Vanessa Neveu, Alice Moussy, Héloïse Rouaix, Roland Wedekind, Allison Pon, Craig Knox, David S. Wishart, Augustin Scalbert, Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D979–D984, <a href="https://doi.org/10.1093/nar/gkw980" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gkw980</a></td> </tr> <tr> <td>15</td> <td>FoodDB</td> <td>70,385</td> <td>Natural products are a sebset of FoodDB <a href="https://foodb.ca/" target="_blank" rel="noopener noreferrer">https://foodb.ca/</a></td> </tr> <tr> <td>16</td> <td>GNPS (Global Natural Products Social Molecular Networking)</td> <td>11,103</td> <td>Wang, M., Carver, J., Phelan, V. et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 34, 828–837 (2016). <a href="https://doi.org/10.1038/nbt.3597" target="_blank" rel="noopener noreferrer">https://doi.org/10.1038/nbt.3597</a></td> </tr> <tr> <td>17</td> <td>HIM (Herbal Ingredients in-vivo Metabolism database)</td> <td>1,259</td> <td>Kang, H., Tang, K., Liu, Q. et al. HIM-herbal ingredients in-vivo metabolism database. J Cheminform 5, 28 (2013). <a href="https://doi.org/10.1186/1758-2946-5-28" target="_blank" rel="noopener noreferrer">https://doi.org/10.1186/1758-2946-5-28</a></td> </tr> <tr> <td>18</td> <td>HIT (Herbal Ingredients Targets)</td> <td>530</td> <td>Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Y. Z. Chen, Yixue Li, Zhiwei Cao, HIT: linking herbal active ingredients to targets, Nucleic Acids Research, Volume 39, Issue suppl_1, 1 January 2011, Pages D1055–D1059, <a href="https://doi.org/10.1093/nar/gkq1165" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gkq1165</a></td> </tr> <tr> <td>19</td> <td>Indofine Chemical Company</td> <td>46</td> <td>Natural products are a sebset of Indofine Chemical Company <a href="https://indofinechemical.com/" target="_blank" rel="noopener noreferrer">https://indofinechemical.com/</a></td> </tr> <tr> <td>20</td> <td>InflamNat</td> <td>664</td> <td>Ruihan Zhang, Jing Lin, Yan Zou, Xing-Jie Zhang, and Wei-Lie Xiao Journal of Chemical Information and Modeling 2019 59 (1), 66-73 DOI: 10.1021/acs.jcim.8b00560 <a href="https://doi.org/10.1021/acs.jcim.8b00560" target="_blank" rel="noopener noreferrer">https://doi.org/10.1021/acs.jcim.8b00560</a></td> </tr> <tr> <td>21</td> <td>InPACdb</td> <td>124</td> <td>Vetrivel et al., Bioinformation 4(2): 71-74 (2009) <a href="https://www.bioinformation.net/004/001500042009.htm" target="_blank" rel="noopener noreferrer">https://www.bioinformation.net/004/001500042009.htm</a></td> </tr> <tr> <td>22</td> <td>InterBioScreen Ltd</td> <td>68,372</td> <td>Natural products are a sebset of InterBioScreen Ltd <a href="https://www.ibscreen.com/natural-compounds" target="_blank" rel="noopener noreferrer">https://www.ibscreen.com/natural-compounds</a></td> </tr> <tr> <td>23</td> <td>KNApSaCK</td> <td>48,241</td> <td>Kensuke Nakamura, Naoki Shimura, Yuuki Otabe, Aki Hirai-Morita, Yukiko Nakamura, Naoaki Ono, Md Altaf Ul-Amin, Shigehiko Kanaya, KNApSAcK-3D: A Three-Dimensional Structure Database of Plant Metabolites, Plant and Cell Physiology, Volume 54, Issue 2, February 2013, Page e4, <a href="https://doi.org/10.1093/pcp/pcs186" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/pcp/pcs186</a></td> </tr> <tr> <td>24</td> <td>Lichen Database</td> <td>1,718</td> <td>Olivier-Jimenez, D., Chollet-Krugler, M., Rondeau, D. et al. A database of high-resolution MS/MS spectra for lichen metabolites. Sci Data 6, 294 (2019). <a href="https://doi.org/10.1038/s41597-019-0305-1" target="_blank" rel="noopener noreferrer">https://doi.org/10.1038/s41597-019-0305-1</a></td> </tr> <tr> <td>25</td> <td>Marine Natural Products</td> <td>14,220</td> <td>Gentile, D.; Patamia, V.; Scala, A.; Sciortino, M.T.; Piperno, A.; Rescifina, A. Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study. Mar. Drugs 2020, 18, 225. <a href="https://doi.org/10.3390/md18040225" target="_blank" rel="noopener noreferrer">https://doi.org/10.3390/md18040225</a></td> </tr> <tr> <td>26</td> <td>Mitishamba database</td> <td>1,095</td> <td>Derese, Solomon., Ndakala, Albert .,Rogo, Michael., Maynim, cholastica and Oyim, James (2015). Mitishamba database: a web based in silico database of natural products from Kenya plants. The 16th symposium of the natural products reseach network for eastern and central Africa (NAPRECA) 31st August to 3rd September 2015 Arusha, Tanzania <a href="http://erepository.uonbi.ac.ke/handle/11295/92273" target="_blank" rel="noopener noreferrer">http://erepository.uonbi.ac.ke/handle/11295/92273</a></td> </tr> <tr> <td>27</td> <td>NANPDB (Natural Products from Northern African Sources)</td> <td>7,482</td> <td>Fidele Ntie-Kang, Kiran K. Telukunta, Kersten Döring, Conrad V. Simoben, Aurélien F. A. Moumbock, Yvette I. Malange, Leonel E. Njume, Joseph N. Yong, Wolfgang Sippl, and Stefan Günther Journal of Natural Products 2017 80 (7), 2067-2076 DOI: 10.1021/acs.jnatprod.7b00283 <a href="https://doi.org/10.1021/acs.jnatprod.7b00283" target="_blank" rel="noopener noreferrer">https://doi.org/10.1021/acs.jnatprod.7b00283</a></td> </tr> <tr> <td>28</td> <td>NCI DTP data</td> <td>419</td> <td>Natural products are a sebset of NCI DTP data <a href="https://wiki.nci.nih.gov/display/NCIDTPdata/Compound+Sets" target="_blank" rel="noopener noreferrer">https://wiki.nci.nih.gov/display/NCIDTPdata/Compound+Sets</a></td> </tr> <tr> <td>29</td> <td>NPACT</td> <td>1,572</td> <td>Manu Mangal, Parul Sagar, Harinder Singh, Gajendra P. S. Raghava, Subhash M. Agarwal, NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database, Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1124–D1129, <a href="https://doi.org/10.1093/nar/gks1047" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gks1047</a></td> </tr> <tr> <td>30</td> <td>NPASS</td> <td>96,173</td> <td>Xian Zeng, Peng Zhang, Weidong He, Chu Qin, Shangying Chen, Lin Tao, Yali Wang, Ying Tan, Dan Gao, Bohua Wang, Zhe Chen, Weiping Chen, Yu Yang Jiang, Yu Zong Chen, NPASS: natural product activity and species source database for natural product research, discovery and tool development, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D1217–D1222, <a href="https://doi.org/10.1093/nar/gkx1026" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gkx1026</a></td> </tr> <tr> <td>31</td> <td>NPAtlas</td> <td>36,395</td> <td>Jeffrey A. van Santen, Grégoire Jacob, Amrit Leen Singh, Victor Aniebok, Marcy J. Balunas, Derek Bunsko, Fausto Carnevale Neto, Laia Castaño-Espriu, Chen Chang, Trevor N. Clark, Jessica L. Cleary Little, David A. Delgadillo, Pieter C. Dorrestein, Katherine R. Duncan, Joseph M. Egan, Melissa M. Galey, F.P. Jake Haeckl, Alex Hua, Alison H. Hughes, Dasha Iskakova, Aswad Khadilkar, Jung-Ho Lee, Sanghoon Lee, Nicole LeGrow, Dennis Y. Liu, Jocelyn M. Macho, Catherine S. McCaughey, Marnix H. Medema, Ram P. Neupane, Timothy J. O’Donnell, Jasmine S. Paula, Laura M. Sanchez, Anam F. Shaikh, Sylvia Soldatou, Barbara R. Terlouw, Tuan Anh Tran, Mercia Valentine, Justin J. J. van der Hooft, Duy A. Vo, Mingxun Wang, Darryl Wilson, Katherine E. Zink, and Roger G. Linington ACS Central Science 2019 5 (11), 1824-1833 DOI: 10.1021/acscentsci.9b00806 <a href="https://doi.org/10.1021/acscentsci.9b00806" target="_blank" rel="noopener noreferrer">https://doi.org/10.1021/acscentsci.9b00806</a></td> </tr> <tr> <td>32</td> <td>NPCARE</td> <td>1,446</td> <td>Choi, H., Cho, S.Y., Pak, H.J. et al. NPCARE: database of natural products and fractional extracts for cancer regulation. J Cheminform 9, 2 (2017). <a href="https://doi.org/10.1186/s13321-016-0188-5" target="_blank" rel="noopener noreferrer">https://doi.org/10.1186/s13321-016-0188-5</a></td> </tr> <tr> <td>33</td> <td>NPEdia</td> <td>49,597</td> <td>Takeshi Tomiki, Tamio Saito, Masashi Ueki, Hideaki Konno, Takeo Asaoka, Ryuichiro Suzuki, Masakazu Uramoto, Hideaki Kakeya, Hiroyuki Osada, [Special Issue: Fact Databases and Freewares] RIKEN Natural Products Encyclopedia (RIKEN NPEdia),a Chemical Database of RIKEN Natural Products Depository (RIKEN NPDepo), Journal of Computer Aided Chemistry, 2006, Volume 7, Pages 157-162, Released on J-STAGE September 15, 2006, Online ISSN 1345-8647, <a href="https://doi.org/10.2751/jcac.7.157" target="_blank" rel="noopener noreferrer">https://doi.org/10.2751/jcac.7.157</a></td> </tr> <tr> <td>34</td> <td>NuBBEDB</td> <td>2,215</td> <td>Pilon, A.C., Valli, M., Dametto, A.C. et al. NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity. Sci Rep 7, 7215 (2017). <a href="https://doi.org/10.1038/s41598-017-07451-x" target="_blank" rel="noopener noreferrer">https://doi.org/10.1038/s41598-017-07451-x</a></td> </tr> <tr> <td>35</td> <td>p-ANAPL</td> <td>533</td> <td>Fidele Ntie-Kang ,Pascal Amoa Onguéné ,Ghislain W. Fotso,Kerstin Andrae-Marobela ,Merhatibeb Bezabih,Jean Claude Ndom,Bonaventure T. Ngadjui,Abiodun O. Ogundaini,Berhanu M. Abegaz,Luc Mbaze Meva’a Published: March 5, 2014 <a href="https://doi.org/10.1371/journal.pone.0090655" target="_blank" rel="noopener noreferrer">https://doi.org/10.1371/journal.pone.0090655</a></td> </tr> <tr> <td>36</td> <td>Phenol-explorer</td> <td>742</td> <td>Joseph A. Rothwell, Jara Perez-Jimenez, Vanessa Neveu, Alexander Medina-Remón, Nouha M'Hiri, Paula García-Lobato, Claudine Manach, Craig Knox, Roman Eisner, David S. Wishart, Augustin Scalbert, Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content, Database, Volume 2013, 2013, bat070, <a href="https://doi.org/10.1093/database/bat070" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/database/bat070</a></td> </tr> <tr> <td>37</td> <td>PubChem NPs</td> <td>3,533</td> <td>Natural products are a sebset of PubChem NPs <a href="https://pubchem.ncbi.nlm.nih.gov/substance/251960601" target="_blank" rel="noopener noreferrer">https://pubchem.ncbi.nlm.nih.gov/substance/251960601</a></td> </tr> <tr> <td>38</td> <td>ReSpect</td> <td>4,854</td> <td>Yuji Sawada, Ryo Nakabayashi, Yutaka Yamada, Makoto Suzuki, Muneo Sato, Akane Sakata, Kenji Akiyama, Tetsuya Sakurai, Fumio Matsuda, Toshio Aoki, Masami Yokota Hirai, Kazuki Saito, RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database, Phytochemistry, Volume 82, 2012, Pages 38-45, ISSN 0031-9422, <a href="https://doi.org/10.1016/j.phytochem.2012.07.007" target="_blank" rel="noopener noreferrer">https://doi.org/10.1016/j.phytochem.2012.07.007</a>.</td> </tr> <tr> <td>39</td> <td>SANCDB</td> <td>995</td> <td>Hatherley, R., Brown, D.K., Musyoka, T.M. et al. SANCDB: a South African natural compound database. J Cheminform 7, 29 (2015). <a href="https://doi.org/10.1186/s13321-015-0080-8" target="_blank" rel="noopener noreferrer">https://doi.org/10.1186/s13321-015-0080-8</a></td> </tr> <tr> <td>40</td> <td>Seaweed Metabolite Database (SWMD)</td> <td>1,075</td> <td>Davis & Vasanthi, Bioinformation 5(8): 361-364 (2011) <a href="https://www.bioinformation.net/005/007900052011.htm" target="_blank" rel="noopener noreferrer">https://www.bioinformation.net/005/007900052011.htm</a></td> </tr> <tr> <td>41</td> <td>Specs Natural Products</td> <td>744</td> <td>Natural products are a sebset of Specs Natural Products <a href="https://www.specs.net/index.php" target="_blank" rel="noopener noreferrer">https://www.specs.net/index.php</a></td> </tr> <tr> <td>42</td> <td>Spektraris NMR</td> <td>248</td> <td>Justin T. Fischedick, Sean R. Johnson, Raymond E.B. Ketchum, Rodney B. Croteau, B. Markus Lange, NMR spectroscopic search module for Spektraris, an online resource for plant natural product identification – Taxane diterpenoids from Taxus×media cell suspension cultures as a case study, Phytochemistry, Volume 113, 2015, Pages 87-95, ISSN 0031-9422, <a href="https://doi.org/10.1016/j.phytochem.2014.11.020" target="_blank" rel="noopener noreferrer">https://doi.org/10.1016/j.phytochem.2014.11.020</a>.</td> </tr> <tr> <td>43</td> <td>StreptomeDB</td> <td>6,522</td> <td>Aurélien F A Moumbock, Mingjie Gao, Ammar Qaseem, Jianyu Li, Pascal A Kirchner, Bakoh Ndingkokhar, Boris D Bekono, Conrad V Simoben, Smith B Babiaka, Yvette I Malange, Florian Sauter, Paul Zierep, Fidele Ntie-Kang, Stefan Günther, StreptomeDB 3.0: an updated compendium of streptomycetes natural products, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D600–D604, <a href="https://doi.org/10.1093/nar/gkaa868" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gkaa868</a></td> </tr> <tr> <td>44</td> <td>Super Natural II</td> <td>325,149</td> <td>Priyanka Banerjee, Jevgeni Erehman, Björn-Oliver Gohlke, Thomas Wilhelm, Robert Preissner, Mathias Dunkel, Super Natural II—a database of natural products, Nucleic Acids Research, Volume 43, Issue D1, 28 January 2015, Pages D935–D939, <a href="https://doi.org/10.1093/nar/gku886" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gku886</a></td> </tr> <tr> <td>45</td> <td>TCMDB@Taiwan (Traditional Chinese Medicine database)</td> <td>58,401</td> <td>Calvin Yu-Chian Chen Published: January 6, 2011 <a href="https://doi.org/10.1371/journal.pone.0015939" target="_blank" rel="noopener noreferrer">https://doi.org/10.1371/journal.pone.0015939</a></td> </tr> <tr> <td>46</td> <td>TCMID (Traditional Chinese Medicine Integrated Database)</td> <td>32,038</td> <td>Xue R, Fang Z, Zhang M, Yi Z, Wen C, Shi T. TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res. 2013 Jan;41(Database issue):D1089-95. doi: 10.1093/nar/gks1100. Epub 2012 Nov 29. PMID: 23203875; PMCID: PMC3531123.</td> </tr> <tr> <td>47</td> <td>TIPdb (database of Taiwan indigenous plants)</td> <td>8,838</td> <td>Chun-Wei Tung, Ying-Chi Lin, Hsun-Shuo Chang, Chia-Chi Wang, Ih-Sheng Chen, Jhao-Liang Jheng, Jih-Heng Li, TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants, Database, Volume 2014, 2014, bau055, <a href="https://doi.org/10.1093/database/bau055" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/database/bau055</a></td> </tr> <tr> <td>48</td> <td>TPPT (Toxic Plants–PhytoToxins)</td> <td>1,561</td> <td>Barbara F. Günthardt, Juliane Hollender, Konrad Hungerbühler, Martin Scheringer, and Thomas D. Bucheli Journal of Agricultural and Food Chemistry 2018 66 (29), 7577-7588 DOI: 10.1021/acs.jafc.8b01639 <a href="https://pubs.acs.org/doi/10.1021/acs.jafc.8b01639" target="_blank" rel="noopener noreferrer">https://pubs.acs.org/doi/10.1021/acs.jafc.8b01639</a></td> </tr> <tr> <td>49</td> <td>UEFS (Natural Products Databse of the UEFS)</td> <td>503</td> <td>Natural products are a sebset of UEFS (Natural Products Databse of the UEFS) <a href="https://zinc12.docking.org/catalogs/uefsnp" target="_blank" rel="noopener noreferrer">https://zinc12.docking.org/catalogs/uefsnp</a></td> </tr> <tr> <td>50</td> <td>UNPD (Universal Natural Products Database)</td> <td>213,210</td> <td>Jiangyong Gu,Yuanshen Gui,Lirong Chen ,Gu Yuan,Hui-Zhe Lu,Xiaojie Xu Published: April 25, 2013 <a href="https://doi.org/10.1371/journal.pone.0062839" target="_blank" rel="noopener noreferrer">https://doi.org/10.1371/journal.pone.0062839</a></td> </tr> <tr> <td>51</td> <td>VietHerb</td> <td>5,150</td> <td>Thanh-Hoang Nguyen-Vo, Tri Le, Duy Pham, Tri Nguyen, Phuc Le, An Nguyen, Thanh Nguyen, Thien-Ngan Nguyen, Vu Nguyen, Hai Do, Khang Trinh, Hai Trong Duong, and Ly Le Journal of Chemical Information and Modeling 2019 59 (1), 1-9 DOI: 10.1021/acs.jcim.8b00399 <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.8b00399" target="_blank" rel="noopener noreferrer">https://pubs.acs.org/doi/10.1021/acs.jcim.8b00399</a></td> </tr> <tr> <td>52</td> <td>ZINC NP</td> <td>85,201</td> <td>Teague Sterling and John J. Irwin Journal of Chemical Information and Modeling 2015 55 (11), 2324-2337 DOI: 10.1021/acs.jcim.5b00559 <a href="https://doi.org/10.1021/acs.jcim.5b00559" target="_blank" rel="noopener noreferrer">https://doi.org/10.1021/acs.jcim.5b00559</a></td> </tr> <tr> <td>53</td> <td>CyanoMetNP</td> <td>2,113</td> <td>Jones MR, Pinto E, Torres MA, Dörr F, Mazur-Marzec H, Szubert K, Tartaglione L, Dell'Aversano C, Miles CO, Beach DG, McCarron P, Sivonen K, Fewer DP, Jokela J, Janssen EM. CyanoMetDB, a comprehensive public database of secondary metabolites from cyanobacteria. Water Res. 2021 May 15;196:117017. doi: 10.1016/j.watres.2021.117017. Epub 2021 Mar 8. PMID: 33765498.</td> </tr> <tr> <td>54</td> <td>DrugBankNP</td> <td>9,283</td> <td>Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, Sajed T, Johnson D, Li C, Sayeeda Z, Assempour N, Iynkkaran I, Liu Y, Maciejewski A, Gale N, Wilson A, Chin L, Cummings R, Le D, Pon A, Knox C, Wilson M. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2017 Nov 8. doi: 10.1093/nar/gkx1037.</td> </tr> <tr> <td>55</td> <td>Australian natural products</td> <td>21,591</td> <td>Saubern, Simon; Shmaylov, Alex; Locock, Katherine; McGilvery, Don; Collins, David (2023): Australian Natural Products dataset. v5. CSIRO. Data Collection. <a href="https://doi.org/10.25919/v8wq-mr81" target="_blank" rel="noopener noreferrer">https://doi.org/10.25919/v8wq-mr81</a></td> </tr> <tr> <td>56</td> <td>EMNPD</td> <td>6,145</td> <td>Xu, HQ., Xiao, H., Bu, JH. et al. EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances. J Cheminform 15, 115 (2023). <a href="https://doi.org/10.1186/s13321-023-00779-9" target="_blank" rel="noopener noreferrer">https://doi.org/10.1186/s13321-023-00779-9</a></td> </tr> <tr> <td>57</td> <td>ANPDB</td> <td>7,482</td> <td>1) Pharmacoinformatic investigation of medicinal plants from East Africa Conrad V. Simoben, Ammar Qaseem, Aurélien F. A. Moumbock, Kiran K. Telukunta, Stefan Günther, Wolfgang Sippl, and Fidele Ntie-Kang Molecular Informatics 2020 DOI: 10.1002/minf.202000163 <a href="https://doi.org/10.1002/minf.202000163" target="_blank" rel="noopener noreferrer">https://doi.org/10.1002/minf.202000163</a> 2) NANPDB: A Resource for Natural Products from Northern African Sources Fidele Ntie-Kang, Kiran K. Telukunta, Kersten Döring, Conrad V. Simoben, Aurélien F. A. Moumbock, Yvette I. Malange, Leonel E. Njume, Joseph N. Yong, Wolfgang Sippl, and Stefan Günther Journal of Natural Products 2017 DOI: 10.1021/acs.jnatprod.7b00283 <a href="https://pubs.acs.org/doi/10.1021/acs.jnatprod.7b00283" target="_blank" rel="noopener noreferrer">https://pubs.acs.org/doi/10.1021/acs.jnatprod.7b00283</a></td> </tr> <tr> <td>58</td> <td>Phyto4Health</td> <td>3,175</td> <td>Nikita Ionov, Dmitry Druzhilovskiy, Dmitry Filimonov, and Vladimir Poroikov Journal of Chemical Information and Modeling 2023 63 (7), 1847-1851 DOI: 10.1021/acs.jcim.2c01567 <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.2c01567" target="_blank" rel="noopener noreferrer">https://pubs.acs.org/doi/10.1021/acs.jcim.2c01567</a></td> </tr> <tr> <td>59</td> <td>Piella DB</td> <td>65</td> <td>Natural products are a sebset of Piella DB <a href="https://micro.biol.ethz.ch/research/piel.html" target="_blank" rel="noopener noreferrer">https://micro.biol.ethz.ch/research/piel.html</a></td> </tr> <tr> <td>60</td> <td>Watermelon</td> <td>1,526</td> <td>Natural products are a sebset of Watermelon <a href="https://watermelon.naturalproducts.net/" target="_blank" rel="noopener noreferrer">https://watermelon.naturalproducts.net/</a></td> </tr> <tr> <td>61</td> <td>Latin America dataset</td> <td>12,959</td> <td>Gómez-García A, Jiménez DAA, Zamora WJ, Barazorda-Ccahuana HL, Chávez-Fumagalli MÁ, Valli M, Andricopulo AD, Bolzani VDS, Olmedo DA, Solís PN, Núñez MJ, Rodríguez Pérez JR, Valencia Sánchez HA, Cortés Hernández HF, Medina-Franco JL. Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB. Pharmaceuticals (Basel). 2023 Sep 30;16(10):1388. doi: 10.3390/ph16101388. PMID: 37895859; PMCID: PMC10609821.</td> </tr> <tr> <td>62</td> <td>CMNPD</td> <td>31,561</td> <td>Chuanyu Lyu, Tong Chen, Bo Qiang, Ningfeng Liu, Heyu Wang, Liangren Zhang, Zhenming Liu, CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D509–D515, <a href="https://doi.org/10.1093/nar/gkaa763" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/nar/gkaa763</a></td> </tr> <tr> <td>63</td> <td>Supernatural3</td> <td>1,203,509</td> <td>Natural products are a sebset of Supernatural3 <a href="https://academic.oup.com/nar/article/51/D1/D654/6833249" target="_blank" rel="noopener noreferrer">https://academic.oup.com/nar/article/51/D1/D654/6833249</a></td> </tr> <tr> <td> </td> <td>Total Entries</td> <td>2,551,803</td> </tr> </tbody> </table>

Article: Modeling Mouse ICM - Complete Data Bank - Part II

Our study presents a spatial-stochastic model for the gene regulatory network (GRN) and the signaling pathway governing cell-fate differentiation during early mouse embryogenesis, specifically at the blastocyst stage. Departing from biophysics-based models of gene regulation, we perform stochastic simulations of the biochemical processes driving early mouse embryogenesis both at the cell and tissue level. Combining these simulations with state-of-the-art AI-aided inference techniques, we successfully parameterize our model, replicating key experimental observations and providing mechanistic insights into the biochemical interactions giving rise to them. Thanks to the stochastic nature of our approach, we quantify the high robustness of ICM specification to various kinds of noise, and provide quantitative predictions for the effects of diverse experimentally testable perturbations. Altogether, we provide a deeper understanding of the intricate mechanisms driving early cell-fate decisions in mouse embryogenesis, highlighting the synergy of local cellular and broader tissue-scale interactions that shape development.

Article: Modeling Mouse ICM - Complete Data Bank - Part III

Article: Modeling Mouse ICM - Complete Data Bank - Part I