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A resource for benchmarking the usefulness of protein structure models

Daniel Carbajo, Anna Tramontano
2012 BMC Bioinformatics  
Implementation, availability and requirements: Project name: A resource for benchmarking the usefulness of protein structure models.  ...  Conclusions: The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis.  ...  Acknowledgements This work was supported by Award number KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST).  ... 
doi:10.1186/1471-2105-13-188 pmid:22856649 pmcid:PMC3473236 fatcat:ntrr3jy6xzgthi3u43ruboijna

A benchmark testing ground for integrating homology modeling and protein docking

Tanggis Bohnuud, Lingqi Luo, Shoshana J. Wodak, Alexandre M. J. J. Bonvin, Zhiping Weng, Sandor Vajda, Ora Schueler-Furman, Dima Kozakov
2016 Proteins: Structure, Function, and Bioinformatics  
The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations.  ...  Protein docking procedures carry out the task of predicting the structure of a protein-protein complex starting from the known structures of the individual protein components.  ...  Ilya Vakser for useful discussions in the course of developing the benchmark set.  ... 
doi:10.1002/prot.25063 pmid:27172383 pmcid:PMC5817996 fatcat:tsl3zmbz2jdc5nq5gha2wkyury

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design

Shane Ó Conchúir, Kyle A. Barlow, Roland A. Pache, Noah Ollikainen, Kale Kundert, Matthew J. O'Meara, Colin A. Smith, Tanja Kortemme, Yang Zhang
2015 PLoS ONE  
We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art  ...  We present a freely accessible web resource (https://kortemmelab.ucsf.edu/ benchmarks) to guide the development of protocols for protein modeling and design.  ...  We thank Liz Kellogg, Rebecca Alford, and Julia Koehler Leman for support with developing the ΔΔG benchmark, and Amelie Stein for contributions to loop modeling. Author Contributions  ... 
doi:10.1371/journal.pone.0130433 pmid:26335248 pmcid:PMC4559433 fatcat:irmm6s6hp5gutd6hkfopad5evm

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Christine Orengo, Sameer Velankar, Shoshana Wodak, Vincent Zoete, Alexandre M.J.J. Bonvin, Arne Elofsson, K. Anton Feenstra, Dietland L. Gerloff, Thomas Hamelryck, John M. Hancock, Manuela Helmer-Citterich, Adam Hospital (+11 others)
2020 F1000Research  
e.g. for human health, drug and protein design.  ...  It also provides an important link with the genomics community, as structural bioinformaticians also use the extensive sequence data to predict protein structures and their functional sites.  ...  The first section of this article ("Major European contributions in structural bioinformatics") describes the historical impact of European research groups in the field of structural bioinformatics.  ... 
doi:10.12688/f1000research.20559.1 pmid:32566135 pmcid:PMC7284151 fatcat:4um6orxypbcfxfq6uh7ue56fsm

Protein models: The Grand Challenge of protein docking

Ivan Anishchenko, Petras J. Kundrotas, Alexander V. Tuzikov, Ilya A. Vakser
2013 Proteins: Structure, Function, and Bioinformatics  
This article presents such a suite of models built for the benchmark set of the X-ray structures from the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu) by a combination of homology modeling  ...  The sets and the accompanying data provide a comprehensive resource for the development of docking methodology for modeled proteins.  ...  a more adequate benchmarking resource.  ... 
doi:10.1002/prot.24385 pmid:23934791 pmcid:PMC4962618 fatcat:c7gffgpcpvdlbfzesfhy4vk42i

Docking Benchmark Set of Protein Models

Ivan Anishchanka, Petras J. Kundrotas, Alexander V. Tuzikov, Ilya A. Vakser
2014 Biophysical Journal  
Such benchmark set of protein models was developed as part of the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu).  ...  The benchmark sets were used in the assessment of protein docking methodologies. 3317-Pos Board B45 Structural Similarity in Modeling of Homodimers Template-based methods, which utilize known protein structures  ...  Such benchmark set of protein models was developed as part of the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu).  ... 
doi:10.1016/j.bpj.2013.11.3629 fatcat:whyx4jysy5gu7h2i6jw4zy3pwm

DOCKGROUND scoring benchmarks for protein docking [article]

Ian Kotthoff, Petras J Kundrotas, Ilya A Vakser
2021 bioRxiv   pre-print
for a large and diverse set of protein-protein complexes.  ...  Two such protein-protein scoring benchmarks were built for the DOCKGROUND resource, which contains various datasets for the development and testing of protein docking methodologies.  ...  A decoy set of experimentally determined unbound structures from the docking benchmark 4 8 and a decoy set of protein models from the model-model docking benchmark 2.  ... 
doi:10.1101/2021.09.02.458795 fatcat:guabzo4jijd5vglf54co6vdxiu

Three-Dimensional Structure of the 54-Kda Subunit of the Chloroplast Signal Recognition Particle using Molecular Modeling

Rory Henderson, Mercede Furr, Srinivas Jayanthi, Alicia Brown, Robyn Goforth, Ralph Henry, T.K.S. Kumar
2014 Biophysical Journal  
Such benchmark set of protein models was developed as part of the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu).  ...  The benchmark sets were used in the assessment of protein docking methodologies. 3317-Pos Board B45 Structural Similarity in Modeling of Homodimers Template-based methods, which utilize known protein structures  ...  Such benchmark set of protein models was developed as part of the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu).  ... 
doi:10.1016/j.bpj.2013.11.3631 fatcat:osv5kciv35cotorjgtkqjn3cku

A Molecular Dynamics Simulation Study of Outer Membrane Phospholipase a (OMPLA) Structure and Dynamics in an Asymmetric Lipopolysaccharide Membrane

Emilia L. Wu, Patrick J. Fleming, Jeffery B. Klauda, Karen G. Fleming, Wonpil Im
2014 Biophysical Journal  
Such benchmark set of protein models was developed as part of the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu).  ...  The benchmark sets were used in the assessment of protein docking methodologies. 3317-Pos Board B45 Structural Similarity in Modeling of Homodimers Template-based methods, which utilize known protein structures  ...  Such benchmark set of protein models was developed as part of the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu).  ... 
doi:10.1016/j.bpj.2013.11.3632 fatcat:ecyyvhyoira6na4oexhh37gyky

Introduction to the Rosetta Special Collection

Sagar D. Khare, Timothy A. Whitehead, Yang Zhang
2015 PLoS ONE  
The Rosetta macromolecular modeling software is a versatile, rapidly developing set of tools that are now being routinely utilized to address state-of-the-art research challenges in academia and industrial  ...  Every two years, a Rosetta Conference (RosettaCon) special collection describing the results presented at the annual conference by participating RosettaCommons labs is published by the Public Library of  ...  There are three main sets of benchmarks in this resource: tests estimating the energetic effects upon mutation, tests for structure prediction, and ones for protein design.  ... 
doi:10.1371/journal.pone.0144326 pmid:26714017 pmcid:PMC4700992 fatcat:7eyke4jnlzebjmbghe5oeypmma

Structural Similarity in Modeling of Homodimers

Petras Kundrotas, Ilya Vakser, Joël Janin
2014 Biophysical Journal  
Such benchmark set of protein models was developed as part of the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu).  ...  The benchmark sets were used in the assessment of protein docking methodologies. 3317-Pos Board B45 Structural Similarity in Modeling of Homodimers Template-based methods, which utilize known protein structures  ...  Such benchmark set of protein models was developed as part of the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu).  ... 
doi:10.1016/j.bpj.2013.11.3630 fatcat:6mxtextqtvfulola626w54fy4i

Modular Platform for Biomolecular Modeling and Simulations

Dominik Gront
2014 Biophysical Journal  
Such benchmark set of protein models was developed as part of the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu).  ...  The benchmark sets were used in the assessment of protein docking methodologies. 3317-Pos Board B45 Structural Similarity in Modeling of Homodimers Template-based methods, which utilize known protein structures  ...  Such benchmark set of protein models was developed as part of the DOCKGROUND resource (http:// dockground.bioinformatics.ku.edu).  ... 
doi:10.1016/j.bpj.2013.11.3633 fatcat:crkk6swcabci7jqcs2q7nhbkee

Protein models docking benchmark 2

Ivan Anishchenko, Petras J. Kundrotas, Alexander V. Tuzikov, Ilya A. Vakser
2015 Proteins: Structure, Function, and Bioinformatics  
Such structures provide templates for modeling of a large part of the proteome, where individual proteins can be docked by template-free or template-based techniques.  ...  The set should also be large enough to ensure statistical reliability of the benchmarking results. We present a major update of the previously developed benchmark set of protein models.  ...  a statistical significance of the benchmarking, and (b) all complexes in the set are true models, which is essential for the benchmarking authenticity.  ... 
doi:10.1002/prot.24784 pmid:25712716 pmcid:PMC4400263 fatcat:efa44htqlzgftdlzn234shiecq

Simulated unbound structures for benchmarking of protein docking in the Dockground resource

Tatsiana Kirys, Anatoly M. Ruvinsky, Deepak Singla, Alexander V. Tuzikov, Petras J. Kundrotas, Ilya A. Vakser
2015 BMC Bioinformatics  
Results: The DOCKGROUND public resource provides data to improve our understanding of protein-protein interactions and to assist in the development of better tools for structural modeling of protein complexes  ...  Conclusions: A radical expansion of the unbound protein docking benchmark set was achieved by simulating the unbound structures.  ...  Acknowledgements The authors are grateful to Huan Rui and Sunhwan Jo for help with CHARMM simulations. This study was supported by NIH grant R01GM074255 and NSF grant DBI1262621.  ... 
doi:10.1186/s12859-015-0672-3 pmid:26227548 pmcid:PMC4521349 fatcat:daakm6aotrby5himvlotq3brc4

Setting up a Meta-Threading Pipeline for High-Throughput Structural Bioinformatics: eThread Software Distribution, Walkthrough and Resource Profiling

Michal Brylinski
2013 Journal of computer science and systems biology  
Depending on the threading algorithm used, the modeling of a single protein sequence of up to 600 residues in length takes minutes to hours.  ...  Abstract eThread, a meta-threading and machine learning-based approach, is designed to effectively identify structural templates for use in protein structure and function modeling from genomic data.  ...  Jason Rappleye, currently Production Engineer at Facebook, for contributing a script for the memory usage profiling.  ... 
doi:10.4172/jcsb.1000094 fatcat:kfma3ewdfngnxfw5iurakwuzkq
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