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9 results for “Surface Evolver”
Supplementary material for "Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors"
<p><strong>Tables</strong></p> <p>Table S1. List of fungal genomes analyzed in this work, associated references and properties.</p> <p>Table S2. List of all secreted proteins less than 300 amino-acids from the 20 fungal genomes. The table includes Signalp4.0 output, mature sequence, Espritz % disorder, pfam domains, AlphaFold top prediction pLDDT and the associated pdb file in Dataset S1.</p> <p>Table S3. Top Hits to pdb database for all OCE structures. 'network_node_name' corresponds to the portein identifier in the OCE structure similarity network provided in Dataset S3. 'Hidef_raw_community' corresponds to groups of structural OCE analogs identified by HiDEF community detection performed on the network provided in Dataset S3.</p> <p>Table S4. Table S4. List of the 62 major OCE folds with associated statistics. Columns I to AB provide the number of occurrences per species. Note that the actual number of members per species might be underestimated due to the stringent pipeline used for OCE identification (excluding proteins larger than 300 amino acids or containing PFAMs for instance).</p> <p> </p> <p>Table S5. Relative surface exposure, conformational flexibility and conservation data mapped on residues of members of the Alt-A1 and BoNT families. RMSD, root mean square deviation for all aligned atoms; Conservation, percentage conservation in multiple structure alignment.</p> <p>Table S6. Assignment of NCBI accessions to MMseqs clusters and assignment of MMseqs clusters to HMM matching-based super-clusters.</p> <p>Table S7. Co-mutation occurrences and associated p-values in two OCE clades from the Alt-A1 and KP6 families.</p> <p>Table S8. Amino acid properties inferred from mutation scans and frustration analyses in Alt-A1 cluster yellow1 and KP6 cluster 43. 'Number of aa variants' corresponds to the number of different amino acids found at each position (deletion counts as 1). 'Alanine scan ∆Z' and 'Deletion scan ∆Z' correspond to the difference between Z-score for the native protein agains itself and Z-score for the native protein against mutant at each position (either Alanine replacement or 5-aa deletion). 'Destabilization factor' is the average of column E and F. 'Stabilization factor' corresponds to the difference between expected structural variation due to destabilization factor and the observed structural variation in multiple mutants. 'netEffect' is difference between column G and H. 'Max co-mutation %' is the highest frequency of co-mutation observed with other residues in natural variants, with 'Min co-mutation p-value (Bonferroni corrected)' the associated p-value.Table S9. Sequence and delta Z of natural variants and mutants from AA1_cl25</p> <p>Table S9. List of natural variants and <em>in silico</em> mutants from the Alt-A1 cluster 25 analyzed in this work, including protein sequence and structure comparison scores (comparison with the reconstructed clade ancestor n0).</p> <p>Table S10. List of natural variants and in silico mutants from the KP6 cluster 43 analyzed in this work, including protein sequence and structure comparison scores (comparison with the reconstructed clade ancestor n0).</p> <p>Table S11. Summary statistics for the phylogenetic trees of 15 OCE clades analyzed for structure and frustration evolution.</p> <p>Table S12. Mapping of structural and frustration data onto phylogenetic trees for 15 OCE clades. The corresponding trees and protein structures are provided in Dataset S7.</p> <p><strong>Datasets</strong></p> <p>Dataset S1. AlphaFold rank1 models for 3 927 OCEs (.pdb format).</p> <p>Dataset S2. Pairwise structure comparison for 3 911 OCE. DALI matrix output containing pairwise Z-scores.</p> <p>Dataset S3. Network file including 2 561 OCEs with 3 or more vertices of Z-score weight 5.2 or more, in .sif and .xgmml formats.</p> <p>Dataset S4. Videos illustrating the mapping of relative surface exposure and structural variability in Alt-A1 and BoNT groups, amino-acids conservation, co-selected mutation patches and residue net stabilization effects on Alt-A1 clade 25 ancestor and KP6 cluster 43 ancestor. Color scales are as in Figure 2 and 3 respectively (.mp4 format).</p> <p>Dataset S5. Phylogenetic trees (.nwk), ancestral (.fasta) and modern variant (.faa) sequences, and AlphaFold best protein models (.pdb) for members of KP6 cluster 43 and Alt-A1 cluster 25. The archive includes 140 Alt-A1 protein structure and 128 KP6 protein structures.</p> <p>Dataset S6. Best predicted structures for 917 natural variants and mutants of AA1_cl25 and 801 natural variants and mutants of KP6_cl43 (.pdb format).</p> <p>Dataset S7. Phylogenetic trees (.nwk) and AlphaFold best protein models (.pdb) for 15 OCE clades. The file includes 2 598 protein structures distributed from clades AA1_s (139), AA1_t (135), AA1_y1 (140), AA1_y2 (90), AA1_y3 (128), BoNT_s (291), CIP_s (167), CIP_t (231), crystallin (233), GNK2 (189), KP6_cl3 (203), KP6_cl26 (111), KP6_cl43 (123), KP6_cl96 (231), KP6_cl242 (187).</p> <p><strong>Text and Figures</strong></p> <p>Text S1. Contains supplementary methods, results and figures S1 to S13.</p>
Surfactant Transport on Evolving Surfaces - Solutions of Space-Time Trace Finite Element Methods visualized.
<p>Videos of numerical experiments in the article "An accurate and robust Eulerian finite element method for partial differential equations on evolving surfaces" by H. Sass and A. Reusken. Surfactant transport on evolving surfaces with high curvatures and topological singularities is illustrated.</p>
Data from: Trunk dental tissue evolved independently from underlying dermal bony plates but is associated to surface bones in living odontode-bearing catfish
Although oral dental tissue is a vertebrate attribute, trunk dental tissue evolved in several extinct vertebrate lineages but is rare among living species. The question of which processes trigger dental-tissue formation in the trunk remains open, and would shed light on odontogenesis evolution. Extra-oral dental structures (odontodes) in the trunk are associated with underlying dermal bony plates, leading us to ask whether the formation of trunk bony plates is necessary for trunk odontodes to emerge. To address this question, we focus on Loricarioidei: an extant, highly diverse group of catfish whose species all have odontodes. We examined the location and cover of odontodes and trunk dermal bony plates for all six loricarioid families and 17 non-loricarioid catfish families for comparison. We inferred the phylogeny of Loricarioidei using a new 10-gene dataset, eight time-calibration points, and noise-reduction techniques. Based on this phylogeny, we reconstructed the ancestral states of odontode and bony plate cover, and find that trunk odontodes emerged before dermal bony plates in Loricarioidei. Yet we discovered that when bony plates are absent, other surface bones are always associated with odontodes, suggesting a link between osteogenic and odontogenic developmental pathways, and indicating a remarkable trunk odontogenic potential in Loricarioidei.
Data from: Trunk dental tissue evolved independently from underlying dermal bony plates but is associated to surface bones in living odontode-bearing catfish
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Data from: A bird’s eye view on turbulence: Seabird foraging associations with evolving surface flow features
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Membrane modeling results from Surface Evolver
<h3>Summary</h3> <p>Three sets of membrane shapes of genus 0 generated in Surface Evolver (Brakke, 1992) are published here. </p> <p>The first set "ZS" reproduces the shapes that were published in Ziherl & Svetina (2005) (bi-layer energy with fixed integrated mean curvature, volume and area). In addition we report on energy values and deliver the shapes as .obj-files. The .dmp files are dumps from the Evolver runs, derived from Frickenhaus (2024).</p> <p>With the same approach, the second set "ST" was created, focusing on axisymmetric stick-like shapes, such as the UnduStick that has been investigated in detail in Frickenhaus & Wölper (2024). </p> <p>The third set "SC" deals with a Helfrich-flow energy functional, where instead of setting a mean curvature constraint, spontaneous curvature $H_0$ enters the bending energy functional.</p> <p>In all three sets energy minimization was done as much as possible, using Newton iteration (hessian_seek) along the surface normals, and gradient decent iterations until energy remained constant. The triangulation was adapted (see command macro gogo in .dmp files) by allowing tangential moves for some steps, equiangulation, vertex averaging, as well as edge length adaptation. File names may indicate non-equilibrium (-ne) or a saddle point (-saddle).</p> <p>Constraint target values are changed in a step-wise manner, writing out the complete data and macros for restarts after every step in a Surface Evolver dump-file automatically. Macros govu and gocu are for volume and curvature change, respectively. dv and dc are the corresponding volume/ curvature change per govo/ gocu cycle. If the triangulation becomes degenerate narrow, it may lead to automatic popping off (budding), i.e. seperation into two bodies. However, quantities volume, curvature and energy are not split up accordingly. </p> <p>The data was created during a project week on Scientific Programming at the University of Bremen, Germany (Mathematics, Summer 2024).</p> <h3>License/ Citation</h3> <p>The data is licensed CC-BY-4.0.</p> <p>When using the code, please cite appropriatly:</p> <p>Frickenhaus, S., Parmar, J. M., Mardomkhah, R., & Asadian, P. (2024). Membrane modeling results from Surface Evolver [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.12805964" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12805964</a></p> <h3>Contributions</h3> <p>RM and PA created the ZS data; JMP created the ST data, and SF created the SC data.</p> <h3>References</h3> <p>K.A. Brakke (1992) The Surface Evolver. Exp. Math. 1(2) <a href="https://dblp.org/db/journals/em/em1.html#Brakke92">https://dblp.org/db/journals/em/em1.html#Brakke92</a> 141-165</p> <p>P. Ziherl and S. Svetina (2005), Nonaxisymmetric phospholipid vesicles: Rackets, boomerangs, and starfish. EPL 70 690, <a href="https://doi.org/10.1209/epl/i2004-10527-4">doi: 10.1209/epl/i2004-10527-4</a></p> <p>S. Frickenhaus, (2024). Exploration of extreme vesicle shapes and their modular structure (1.0). Zenodo. <a href="https://doi.org/10.5281/zenodo.11199344" target="_blank" rel="noopener">doi: 10.5281/zenodo.11199344</a></p> <p>S. Frickenhaus, C. Wölper, (2024). MembraneR - a membrane modeling environment in R (Version 1). Zenodo. <a href="https://doi.org/10.5281/zenodo.12721406" target="_blank" rel="noopener">doi: 10.5281/zenodo.12721406</a></p>
Surface proteomics reveals CD72 as a target for in vitro-evolved nanobody-based CAR-T cells in refractory B-cell malignancies
GEO Series GSE143181. Homo sapiens. 21 samples. Type: Expression profiling by high throughput sequencing; Other.
Surface proteomics reveals CD72 as a target for in vitro-evolved nanobody-based CAR-T cells in refractory B-cell malignancies II
GEO Series GSE143179. Homo sapiens. 4 samples. Type: Other.
Surface proteomics reveals CD72 as a target for in vitro-evolved nanobody-based CAR-T cells in refractory B-cell malignancies I
GEO Series GSE142447. Homo sapiens. 17 samples. Type: Expression profiling by high throughput sequencing.
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