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154 results for “ALA”
Quantum chemical optimizations of Ala-Gly di- and tripeptides
<p>Quantum chemical simulations of reactants and products for aa dimerization</p> <p>Software: Gaussian v16 RevA.03</p> <p>The "thermochemistry" archive refers to thermochemical calculations of reactants and products for condensation of Alanine, Glycine and boric acid. Geometry optimizations were carried out at the B3LYP/6-311G** level of theory, both in vacuo and in water in a polarized continuum fashion. </p> <p>See readme.txt file for a detailed list of files and directories.</p>
Molecular dynamics simulation trajectories of HIV protein gp120 in complex with antibody VRC01 and 30 of its Ala mutants
<p>This data set accompanies the publication by S. Conti, E. Lau, and V. Ovchinnikov entitled "On the rapid calculation of binding affinities for antigen and antibody design and affinity maturation simulations", to be published in the MDPI journal Antibodies. It contains molecular dynamics simulation trajectories of HIV protein gp120 in complex with antibody VRC01 and 30 of its Ala mutants, as described in the paper. The format of the trajectory files is CHARMM-compatible dcd. The files can be visualized with the program Visual Molecular Dynamics (VMD) (see paper by Humphrey et al. 1996, J. Molec. Graphics). The accompanying file "view" is a tcl-based script for VMD that can be executed in the Linux environment using: "vmd -e view", which will display the trajectory of the mutant specified by editing the first noncomment line of the script.<br> </p>
Рис. 1. Ctenoceratoda tancrei, бабочки из разΛичных ΛокаΛитетов: а, e — Киргизский хр., нац. парк «АΛа-Арча»; b, f — хр. ΔжумгаΛтоо, массив Сары-Кайкы; c, d, g, h — хр. МоΛΑо-Тоо, пер. Коро-Гоо. a–d — самцы, e–h — самки Fig. 1. Ctenoceratoda tancrei, the wing pattern variability: a, e — Kirghiz Mts., «Ala-Archa» national park; b, f — Dzhumgaltoo Mts., Sary-Kaiky gorge; c, d, g, h — Moldo-Too Mts., Koro-Goo Pass. a–d — males, e–h — females in Morphometric analysis of genitalia of Ctenoceratoda tancrei (Graeser, 1892) (Lepidoptera, Noctuidae)
Рис. 1. Ctenoceratoda tancrei, бабочки из разΛичных ΛокаΛитетов: а, e — Киргизский хр., нац. парк «АΛа-Арча»; b, f — хр. ΔжумгаΛтоо, массив Сары-Кайкы; c, d, g, h — хр. МоΛΑо-Тоо, пер. Коро-Гоо. a–d — самцы, e–h — самки Fig. 1. Ctenoceratoda tancrei, the wing pattern variability: a, e — Kirghiz Mts., «Ala-Archa» national park; b, f — Dzhumgaltoo Mts., Sary-Kaiky gorge; c, d, g, h — Moldo-Too Mts., Koro-Goo Pass. a–d — males, e–h — females
Рис. 1. Bryoxena centralasiae, изменчивость крыΛового рисунка: а, λ — Киргизский хр., нац. парк «АΛа-Арча»; в, г, з — хр. ΔжумгаΛтоо, массив Сары-Кайкы; д, к, м — хр. МоΛΑо-Тоо, пер. Коро-Гоо; б, е — Ферганский хр., пер. Урумбаш; ж, и — АΛайский хр., пер. ТаΛΑык Fig. 1. Bryoxena centralasiae, the wing pattern variability: а, λ — Kirghiz Mts., «Ala-Archa» national park; в, г, з — Dzhumgaltoo Mts., Sary-Kaiky gorge; д, к, м — Moldo-Too Mts., Koro-Goo Pass; б, е — Fergansky Mts., Urumbash Pass; ж, и — Alai Mts., Taldyk Pass in Morphometric Analysis Of The Genitalia Of (Staudinger, 1882) (Lepidoptera, Noctuidae)
Рис. 1. Bryoxena centralasiae, изменчивость крыΛового рисунка: а, λ — Киргизский хр., нац. парк «АΛа-Арча»; в, г, з — хр. ΔжумгаΛтоо, массив Сары-Кайкы; д, к, м — хр. МоΛΑо-Тоо, пер. Коро-Гоо; б, е — Ферганский хр., пер. Урумбаш; ж, и — АΛайский хр., пер. ТаΛΑык Fig. 1. Bryoxena centralasiae, the wing pattern variability: а, λ — Kirghiz Mts., «Ala-Archa» national park; в, г, з — Dzhumgaltoo Mts., Sary-Kaiky gorge; д, к, м — Moldo-Too Mts., Koro-Goo Pass; б, е — Fergansky Mts., Urumbash Pass; ж, и — Alai Mts., Taldyk Pass
Figuras 6-9. 6. Ala anterior. 7. Tergito abdominal III. 8 in Primer registro de Scirtothrips dorsalis Hood, 1919 (Thysanoptera: Thripidae) en Perú, y su potencial riesgo fitosanitario para la agricultura chilena
Figuras 6-9. 6. Ala anterior. 7. Tergito abdominal III. 8. Microtrichia en esternitos abdominales. 9. Tergitos abdominales del macho. Escala: 0,20 mm. /6. Forewing. 7. Abdominal tergite III. 8. Abdominal sternites with microtrichia. 9. Male abdominal tergites. Scale: 0.20 mm.
Figure 2 in Spatial and temporal nesting pattern of Sea Turtles in Alas Purwo National Park, and its implications for conservation management practices
Figure 2. Trend of sea turtle nesting in the past 40 years at APNP: (A) L.olivacea, (B) C. mydas, (C) E. imbricata, and (D) D. coriacea.
Figure 1 in Spatial and temporal nesting pattern of Sea Turtles in Alas Purwo National Park, and its implications for conservation management practices
Figure 1. Study location in Alas Purwo National Park's Pancur-Cungur Coast with six hypothetical stations (dot: sector benchmark point).
Figure 4 in Spatial and temporal nesting pattern of Sea Turtles in Alas Purwo National Park, and its implications for conservation management practices
Figure 4. Number of four sea turtles nesting in each month during survey period: (A) L.olivacea, (B) C. mydas, (C) E. imbricata, and (D) D. coriacea.
Linked collectors and determiners for: UAM Herbarium (ALA), Algae Collection (Arctos).
Natural history specimen data linked to collectors and determiners held within, "UAM Herbarium (ALA), Algae Collection (Arctos)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/873f843b-7c49-4f00-a842-9107f79213ca">https://bionomia.net/dataset/873f843b-7c49-4f00-a842-9107f79213ca</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/873f843b-7c49-4f00-a842-9107f79213ca">https://gbif.org/dataset/873f843b-7c49-4f00-a842-9107f79213ca</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: UAM Herbarium (ALA), Vascular Plant Collection (Arctos).
Natural history specimen data linked to collectors and determiners held within, "UAM Herbarium (ALA), Vascular Plant Collection (Arctos)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/5c1fdaf6-4a18-4c5d-a84b-a4ba41f077c9">https://bionomia.net/dataset/5c1fdaf6-4a18-4c5d-a84b-a4ba41f077c9</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/5c1fdaf6-4a18-4c5d-a84b-a4ba41f077c9">https://gbif.org/dataset/5c1fdaf6-4a18-4c5d-a84b-a4ba41f077c9</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: UAM Herbarium (ALA), Cryptogam Collection (Arctos).
Natural history specimen data linked to collectors and determiners held within, "UAM Herbarium (ALA), Cryptogam Collection (Arctos)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/39f7ffd7-9416-4efb-934a-c81f116893fc">https://bionomia.net/dataset/39f7ffd7-9416-4efb-934a-c81f116893fc</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/39f7ffd7-9416-4efb-934a-c81f116893fc">https://gbif.org/dataset/39f7ffd7-9416-4efb-934a-c81f116893fc</a>. Formatted as a Frictionless Data package.
Text-fig. 3. Dorsal view of endocranium of armadillo (Dasypus novemcinctus); some dermal allostoses from the right side are included. Derivatives of the teniform cartilage blue. co: orbitoparietal commissure; con: sphenethmoidal (orbitonasal) commissure; ctn: cartilago tecti nasi; lp: parietal lamina; oc: orbital cartilage (ala orbitalis); po: parieto-occipital commissure. (Modified from Reinbach 1952.) in Cartilago Teniformis And Its Derivatives: Additional Information On The Basic Composition And Evolution Of The Skull
Text-fig. 3. Dorsal view of endocranium of armadillo (Dasypus novemcinctus); some dermal allostoses from the right side are included. Derivatives of the teniform cartilage blue. co: orbitoparietal commissure; con: sphenethmoidal (orbitonasal) commissure; ctn: cartilago tecti nasi; lp: parietal lamina; oc: orbital cartilage (ala orbitalis); po: parieto-occipital commissure. (Modified from Reinbach 1952.)
Diffraction data for complex of vancomycin with N-acetyl-D-Ala-D-Ser
<p>Raw diffraction images collected for a single crystal of the glycopeptide antibiotic vancomycin bound to N-acetyl-D-Ala-D-Ser (HDF5 format). Measured at beam line 17-ID-1 (AMX), NSLS-II, in December 2021, using an Eiger 9M detector. Other relevant metadata can be found in the file XDS.INP.</p>
INSCRIPCIÓN DEL CLAUSTRO DE RODA. ALA SUR ARCO 7
INSCRIPCIÓN DE RAIMUNDO EN EL CLAUSTRO Esta inscripción nos informa de la muerte, el 12 de febrero (II IDVS FEBRUARII), de un canónigo y levita llamado Raimundus. Así, todos los años en esa fecha los canónigos de la Catedral, rezarán por el alma de dicha persona, mientras deambulan por el claustro. Escrito con letra mayúscula gótica sobre un marco inciso. Ubicación: Inscripción primera de la séptima arcada en la panda sur. II : IDVS // FEB(rua) RII // OB(iit) RAIM(un)D(us) // CAN(on)ICVS // ET LEVITA Source: Objaverse 1.0 / Sketchfab
Molecular dynamics simulation of MFSD1 in apo, His-Ala, Lys-Ala and Leu-Ala bound
<p>The MFSD1 structures were placed in a heterogenous bilayer composed of POPE (20%), 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC, 30%), Cholesterol (30%), and N-Palmitoyl-sphingomyelin (SPM, 20%) using CHARMM-GUI scripts and all simulations were performed using GROMACS 2021.3. </p> <p>Substrates were fitted into the binding site based on non-protein density observed in the outward-open Cryo-EM structure of GLMP-MFSD1+HisAla. </p> <p>Here, inital structures and 500 ns simulations for each replicate (Rep1-3) with the respective ligands and its starting conformation (Conf1 or Conf2) are given in PDB-format. </p> <p>The following ligands were used for the molecular dynamics simulations:</p> <ul> <li>LA - Leucyl-alanine dipeptide: both termini are charged</li> <li>KA - Lysyl-alanine dipeptide: both termini are charged, side chain of lysine is positively charged</li> <li>H0A - Histidyl-alanine dipeptide: both termini are charged, side chain of histidine is neutral</li> <li>HA - Histidyl-alanine dipeptide: both termini are charged, side chain of histidine is positively charged</li> </ul>
INSCRIPCIÓN CLAUSTRO DE RODA. ALA SUR. ARCO 11
En el claustro de la Catedral de San Vicente en Roda de Isábena, Ribagorza, nos encontramos esta inscripción situada en la panda sur del claustro, cercana a la puerta de acceso al templo. Letra mayúscula gótica, en marco inciso. Nos dice que el 9 de Mayo (VII IDUS MAI), falleció el Prior Amatus, canónigo y sacerdote. Cómo es habitual en las inscripciones del claustro no se indica el año de su muerte, pues se trataba de orar por el difunto en su aniversario. Source: Objaverse 1.0 / Sketchfab
Pedistal, Yesod Hama'ala
Bazalt pedistal from the ancient synagogue and/or sugar refinery in Yesod Hama'ala. Documented by children from the village Source: Objaverse 1.0 / Sketchfab
Ace-Ala-Xaa-Ala-NH2 sasa and Phi,Psi surfaces
<p>******************************************************************************<br> Charles R. Watts Lab <br> Protein Dynamics Data Distribution <br>******************************************************************************</p> <p>Contents<br>--------</p> <p>This directory contains data associated with the research paper titled:</p> <p> Burns,WA;Lovas,S;Watts,CR. "Dynamic Solvent Accessible Surface Areas of Proteogenic α-Amino Acids<br> as a Function of Explored Φ,Ψ Dihedral Angle Space Modeled Using the<br> Ac-Ala-Xaa-Ala-NH2 System and CHARMM36m Force Field" International Journal of Molecular Sciences (IJMS) 2024; Sumbitted</p> <p>from the Charles R. Watts Lab at Healthpartners Institute. The data is organized <br>into multiple CSV files, each containing information about protein dynamics.</p> <p>File Format<br>-----------</p> <p>Each CSV file contains data in the following format:</p> <p> Time,SASA-FULL,SASA-BACKBONE,SASA-SIDECHAIN,Phi,Psi,Residue,CLUSTER<br> <br>The columns are defined as follows:</p> <p> Time : The time point at which the data was recorded.<br> SASA-FULL : Solvent Accessible Surface Area for the full protein.<br> SASA-BACKBONE : Solvent Accessible Surface Area for the protein backbone.<br> SASA-SIDECHAIN : Solvent Accessible Surface Area for the protein side chain.<br> Phi : Dihedral angle Φ.<br> Psi : Dihedral angle Ψ.<br> Residue : The name of the residue being measured and position with zero based indexing.<br> CLUSTER : The secondary structure cluster associated with the residue.</p> <p>Example Data<br>------------</p> <p>Below is an example of the data format:</p> <p> Time,SASA-FULL,SASA-BACKBONE,SASA-SIDECHAIN,Phi,Psi,Residue,CLUSTER<br> 200002.0,104.19,45.93,58.26,-60.4,152.19,ALA-3,Beta<br> 200004.0,103.76,43.14,60.62,-98.82,159.36,ALA-3,Beta<br> 200006.0,102.23,45.05,57.18,-142.54,-179.97,ALA-3,Beta<br> 200008.0,104.6,48.57,56.03,-158.17,158.18,ALA-3,Beta<br> 200010.0,107.55,47.68,59.87,-164.53,157.51,ALA-3,Beta<br> 200012.0,104.79,33.72,71.07,-88.1,113.28,ALA-3,Beta</p> <p>File List<br>---------</p> <p>The following is a list of the CSV files provided in this directory:</p> <p> Ala.csv Arg:NH.csv Asp:H.csv Cys-Cys.csv Glu:H.csv His:ND1.csv Leu.csv Met.csv<br> Arg.csv Asn.csv Cys-.csv Gln.csv Gly.csv His:NE2.csv Lys.csv Phe.csv<br> Arg:NE.csv Asp.csv Cys.csv Glu.csv His+.csv Ile.csv Lysn.csv Pro:cis.csv<br> Arg:NH.csv Asp:H.csv Cys-Cys.csv Glu:H.csv His:ND1.csv Leu.csv Met.csv Pro:trans.csv<br> Trp.csv Tyr-.csv Tyr.csv Ser.csv Thr.csv Val.csv</p> <p>Each file contains similar data but for different residues. There is also a directory inside called Probability Surface. This contains all the smoothed probability of each angular measurment binned to 1 degree and smoothed using the algorithm from Lovell 2003. </p> <p>Usage<br>-----</p> <p>The data can be read into a variety of software packages for further analysis, <br>including but not limited to:</p> <p> - Python (pandas, numpy)<br> - R (data.table, readr)<br> - MATLAB<br> - Microsoft Excel</p> <p>License<br>-------</p> <p>This data is liscences under the Creative Commons Attribution 4.0 International (CC BY 4.0) liscence. You are free to share and adapt the data,<br>provided you give appropriate credit. When using this data, please cite as follows below: <br>The data comes with no warranty, express or implied.<br>please cite the following DOI: 10.5281/zenodo.13137464.</p> <p>Contact<br>-------</p> <p>For any inquiries or issues related to the data, please contact:</p> <p> Charles R. Watts Lab<br> Department of Neurosurgery<br> Healthpartners/Park Nicollet/Methodist Hospital<br> Email: charles.watts@parknicollet.com<br>******************************************************************************</p>
ALA induced transcriptome and single cell microscopy of M.tuberculosis
<p> <strong>Single cell microscopy of porphyeins in vegetative and dormant <em>Mycobacterium tuberculosis</em>. Confocal fluorescence microscopy, life-time measurements, and microspectrofluorimetry. </strong>Fluorescence lifetime measurements were performed on a PicoQuant MicroTime 200 confocal scanning system (Pico-Quant GmbH, Berlin, Germany) based on an Olympus IX-71 inverted fluorescence microscope (Japan). SymphoTime® software was used for data collection. Fluorescence spectra were recorded in the confocal mode of the MicroTime 200 system using a Shamrock 163 spectrograph with a Newton DU-970 camera (Andor, UK).</p> <p><strong>Transcriptomic analysis of cells of <em>M. tuberculosis </em>in a vegetative state and under transition into dormant state upon administration of exogenous ALA.</strong> The quality of the resulting libraries was checked using the Fragment Analyzer. Quantitative analysis was performed by qPCR. After quality control and assessment of DNA quantity, the pool of libraries was sequenced on an Illumina NovaSeq 6000 instrument (length of reads - 150 bp on both sides of the fragments). FASTQ files were generated using bcl2fastq v2.20 Conversion Software (Illumina). The quality data string record format is Phred 33. As a result, 1,107,614,502 reads were received. </p> <pre>This study was funded by Russian Science Foundation grant 19-15-00324.</pre>
Trench in WW1 base, Ala-Malmi, Helsinki, Finland
Trench in First World War base XI:2 in [Krepost Sveaborg](https://en.wikipedia.org/wiki/Krepost_Sveaborg) land front defense line in Ala-Malmi, Helsinki, Finland. The base was built in 1915 - 1918. There is also additional models from this same base XI:2: * [Observation post](https://skfb.ly/6UWDx) * [Tunnels](https://skfb.ly/6UCqO) * [Cave entrance](https://skfb.ly/6UCqV) More info: * [Location in Google Maps](https://goo.gl/maps/tRFvMkRRfcoRaJ548) * [Wikipedia: Krepost Sveaborg](https://en.wikipedia.org/wiki/Krepost_Sveaborg) * [John Lagerstedt , Markku Saari: Krepost Sveaborg](http://www.novision.fi/viapori/eavaus.htm) * [Finnish Heritage Agency site info](https://www.kyppi.fi/to.aspx?id=112.1000013430) (only in finnish) Source: Objaverse 1.0 / Sketchfab
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