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Practical use of a fully automatic homology-based protein modelling protocol

E. Platt, B. Robson
Proceedings of the Twenty-Eighth Hawaii International Conference on System Sciences, vol.5  
A j&lly automatic protocol HOM-FOLD for modelling proteins by homology, using a fragment based approach, is described. The present report describes the performance of the basic algorithm.  ...  The protocol was intended to be, and is normally used as, a first step only, with more elaborate algorithms for energy refinement to be applied subsequently in the context of a higher l&Tel protocol.  ...  METHOD 3.1 STEP 1: Preliminary fit-based modelling of the RMS aligned blocks Modelling is automatically initiated :- (i) I3y extracting the Ca co-ordinates and dihedral angles of the Template protein of  ... 
doi:10.1109/hicss.1995.375323 dblp:conf/hicss/PlattR95 fatcat:volbxfyhwfhktdtq252sskl6v4

PDBalert: automatic, recurrent remote homology tracking and protein structure prediction

Vatsal Agarwal, Michael Remmert, Andreas Biegert, Johannes Söding
2008 BMC Structural Biology  
Results: PDBalert is a web-based automatic system that sends an email alert as soon as a structure with homology to a protein in the user's watch list is released to the PDB database or appears among the  ...  Automatic structure prediction servers relying on these methods can generate useful 3D models even below 20% sequence identity between the protein of interest and the known structure (template).  ...  PDBalert is a new web-based automatic system for protein homology detection, which checks the PDB database every week for templates homologous to the proteins in the users' watch lists.  ... 
doi:10.1186/1472-6807-8-51 pmid:19025670 pmcid:PMC2605448 fatcat:kzw7ezysk5e6rcgbefc2g3gxti

Building and Refining Protein Models within Cryo-electron Microscopy Density Maps Based on Homology Modeling and Multiscale Structure Refinement

Jiang Zhu, Lingpeng Cheng, Qin Fang, Z. Hong Zhou, Barry Honig
2010 Journal of Molecular Biology  
An EM-IMO-based refinement protocol is first benchmarked on a data set of 50 homology models using simulated density maps.  ...  Our study demonstrates that the integrated use of homology modeling and a multi-scale refinement protocol that combines supervised and automated structure refinement offers a practical strategy for building  ...  MCB-0416708 to BH), National Basic Research Program of China (973 Program #2009CB118701 to QF), National Natural Scientific Foundation of China (30671615 and 30871940 to QF) and the Chinese Academy of  ... 
doi:10.1016/j.jmb.2010.01.041 pmid:20109465 pmcid:PMC2860449 fatcat:ki6l3g343vc3bo3ijyms74fufa

HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm

Pei Zhou, Bowen Jin, Hao Li, Sheng-You Huang
2018 Nucleic Acids Research  
HPEPDOCK also performed well in docking against homology models and obtained a success rate of 29.8% within top 10 predictions.  ...  For local peptide docking, HPEPDOCK achieved a high success rate of 72.6% on a benchmark of 62 unbound cases within top 10 predictions, compared to 45.2% for HADDOCK peptide protocol.  ...  In addition, if only a sequence is provided as the input for a protein, the result page will also show the information of the protein model built by homology modeling, including the used template, and  ... 
doi:10.1093/nar/gky357 pmid:29746661 pmcid:PMC6030929 fatcat:44izrgjpevbjlamb7n57fckdkq

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information

Lenka Sumbalova, Jan Stourac, Tomas Martinek, David Bednar, Jiri Damborsky
2018 Nucleic Acids Research  
The protein structure for the query sequence is obtained either from eight repositories of homology models or is modeled using Modeller and I-Tasser.  ...  During follow-up analyses, the system automatically warns the users whenever they attempt to redesign poorly predicted parts of their homology models.  ...  FUNDING Ministry of Education, Youth and Sports of the Czech  ... 
doi:10.1093/nar/gky417 pmid:29796670 pmcid:PMC6030891 fatcat:qenwbseu3zg3hgkyabrd52rthq

Methods for Sequence–Structure Alignment [chapter]

Česlovas Venclovas
2011 Msphere  
Hence, a homology model of a protein can be derived using related protein structure(s) as modeling template(s).  ...  Homology modeling is based on the observation that related protein sequences adopt similar three-dimensional structures.  ...  Acknowledgments Ana Vencloviené and members of Venclovas' lab are gratefully acknowledged for useful comments and suggestions.  ... 
doi:10.1007/978-1-61779-588-6_3 pmid:22323217 fatcat:fvv6qwx3lrh2lbmgy55ejmre6q

Convergent evolution of protein structure prediction and computer chess tournaments: CASP, Kasparov, and CAFASP

N. Siew, D. Fischer
2001 IBM Systems Journal  
A limitation of CASP is that predictions are prepared and filed by humans using programs, and thus, what is being evaluated is the performance of the predicting groups rather than the performance of the  ...  Predicting the three-dimensional structure of a protein from its amino acid sequence is one of the most important current problems of modern biology.  ...  In homology modeling, a template is a protein of known 3-D structure with enough sequence similarity to the sequence of the target protein.  ... 
doi:10.1147/sj.402.0410 fatcat:ejejbjkfa5ddzfaqjkfbxb5zwi

RBO Aleph: leveraging novel information sources for protein structure prediction

Mahmoud Mabrouk, Ines Putz, Tim Werner, Michael Schneider, Moritz Neeb, Philipp Bartels, Oliver Brock
2015 Nucleic Acids Research  
Based on template availability, RBO Aleph switches automatically between template-based modeling and ab initio prediction based on the target protein sequence, facilitating use especially for non-expert  ...  RBO Aleph is a novel protein structure prediction web server for template-based modeling, protein contact prediction and ab initio structure prediction.  ...  If good templates are identified, our server performs homology modeling with MODELLER ( 14 ) and then uses a loop modeling protocol (15) to remodel parts of the protein not covered by the templates.  ... 
doi:10.1093/nar/gkv357 pmid:25897112 pmcid:PMC4489312 fatcat:jfhc77yhjzbg7axvvd67ep2brm

InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs

Chloé Quignot, Julien Rey, Jinchao Yu, Pierre Tufféry, Raphaël Guerois, Jessica Andreani
2018 Nucleic Acids Research  
For this purpose, we added modules in InterEvDock2 for automatic template search and comparative modeling of the input proteins.  ...  We previously developed InterEvDock, a server for ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore  ...  To handle sequence inputs, we have added a module that performs comparative modeling prior to docking based on an automatic template search protocol.  ... 
doi:10.1093/nar/gky377 pmid:29741647 pmcid:PMC6030979 fatcat:uo5hymzxmbd7jion6euir637u4

Reconstruction of genome-scale metabolic model for Hansenula polymorpha using RAVEN toolbox [article]

Francisco Zorrilla, Eduard J Kerkhoven
2021 bioRxiv   pre-print
Using the RAVEN toolbox, this protocol practically demonstrates how researchers can create their own GEMs using a homology based approach.  ...  Genome scale metabolic models (GEMs) provide a useful framework for modeling the metabolism of microorganisms.  ...  The following protocol demonstrates a practical implementation of the various steps necessary for the homology--based reconstruction of GEMs using the RAVEN toolbox.  ... 
doi:10.1101/2021.06.18.448943 fatcat:fwr2ux5iwna3xhqr3jidwewt5m

Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies

Daria Timonina, Yana Sharapova, Vytas Švedas, Dmitry Suplatov
2021 Computational and Structural Biotechnology Journal  
A companion Mustguseal web-server is available to automatically construct a 3D-alignment of functionally diverse proteins, thus reducing the minimal input required to operate Zebra3D to a single PDB code  ...  We have developed Zebra3D - the first-of-its-kind bioinformatic software for systematic analysis of 3D-alignments of protein families using machine learning.  ...  The use of HPC computing resources at the Lomonosov Moscow State University to accelerate the evaluation of Zebra3D during its development is acknowledged [89] .  ... 
doi:10.1016/j.csbj.2021.02.005 pmid:33738079 pmcid:PMC7933735 fatcat:wrgsazud3jhivghmwlnarnt3bi

Automated refinement of macromolecular structures at low resolution using prior information

Oleg Kovalevskiy, Robert A. Nicholls, Garib N. Murshudov
2016 Acta Crystallographica Section D: Structural Biology  
After running extensive tests on a large data set of low-resolution models, the best-performing refinement protocols and strategies for the selection of homologous structures have been identified.  ...  These restraints are used byREFMAC5 to stabilize the refinement of an atomic model.  ...  We also thank the LMB for creating a very active working environment.  ... 
doi:10.1107/s2059798316014534 pmid:27710936 pmcid:PMC5053141 fatcat:lpfyl2jrabfslcayi55lwrkuuq

High-Accuracy Protein Structures By Combining Machine-Learning With Physics-Based Refinement [article]

Lim Heo, Michael Feig
2019 bioRxiv   pre-print
Protein structure prediction has long been available as an alternative to experimental structure determination, especially via homology modeling based on templates from related sequences.  ...  Here we show that combining machine-learning based models from AlphaFold with state-of-the-art physics-based refinement via molecular dynamics simulations further improves predictions to outperform any  ...  This research was supported by National Institutes of Health Grants R01 GM084953 and R35 GM126948.  ... 
doi:10.1101/731521 fatcat:y6k7qlgaivd73hpimxue24vpyi

Computational Methods in Mass Spectrometry-Based Protein 3D Studies [chapter]

Rosa M., Giovanni Renzone, Andrea Scaloni, Pietro Amodeo
2011 Computational Biology and Applied Bioinformatics  
A successful examples of modelling with MS-based information in a low-homology case is Gadd45β.  ...  As in protein folding, also for docking the use of MS-based information allowed the modelling of several complexes even in the lack of suitable templates with high homology.  ... 
doi:10.5772/19635 fatcat:avrh2hfmcjhstpilvhxc32jcvu

Functional prediction through phylogenetic inference and structural classification of proteins [chapter]

Kimmen Sj��lander, Chelsea Specht
2006 Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics  
Acknowledgments This work was supported in part by Grant #0238311 from the National Science Foundation, and by Grant #R01 HG002769-01 from the National Institutes of Health to KS.  ...  Bayesian methods promise to reduce the time necessary for a model-based approach using Markov-chain Monte Carlo simulations of character space.  ...  Controversy surrounds the selection of a prior and its overall contribution to the resulting tree topology; however, the use of Markovchain Monte Carlo algorithms to rapidly explore tree space makes model-based  ... 
doi:10.1002/047001153x.g306320 fatcat:hfc4hxrpgbempbltbb223ul4pi
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