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FreeContact: fast and free software for protein contact prediction from residue co-evolution

László Kaján, Thomas A Hopf, Matúš Kalaš, Debora S Marks, Burkhard Rost
2014 BMC Bioinformatics  
20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions  ...  FreeContact supports the BioXSD format for interoperability. Conclusions: FreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud).  ...  We thank Timothy Karl (TUM) for invaluable help with hardware and software and Marlena Drabik (TUM) for administrative support.  ... 
doi:10.1186/1471-2105-15-85 pmid:24669753 pmcid:PMC3987048 fatcat:l5b2jxuwb5hhlk342h5x2oonsq

Performance Analysis of Deep Learning Methods for Protein Contact Prediction in CASP13

Romina Valdez, Khevin Roig, Diego P. Pinto-Roa, Jose Colbes
2021 CLEI Electronic Journal  
The set of proteins used for the experiments and the implementations made for the analysis are publicly available.  ...  For the contact prediction category, the best methods in CASP13 achieved an average precision of 70%.  ...  Marks, and B. Rost, “Freecontact: fast and free software for protein contact prediction from residue co-evolution,” BMC bioinformatics, vol. 15, no. 1, p. 85, 2014. [17] H. Kamisetty, S.  ... 
doi:10.19153/cleiej.24.2.3 fatcat:psdbvnrhizayvfsfgx73rp54ta

I-COMS: Interprotein-COrrelated Mutations Server

Javier Iserte, Franco L. Simonetti, Diego J. Zea, Elin Teppa, Cristina Marino-Buslje
2015 Nucleic Acids Research  
Interprotein contact prediction using multiple sequence alignments (MSAs) is a useful approach to help detect protein-protein interfaces.  ...  I-COMS allows to estimate covariation between residues of different proteins by four different covariation methods.  ...  Here we present a server that allows users to analyze coevolutionary relationships between groups of proteins with four state of the art co-evolution algorithms: precise structural contact prediction using  ... 
doi:10.1093/nar/gkv572 pmid:26032772 pmcid:PMC4489276 fatcat:keg7zur4jjhlnfje7ds75qc5tm

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

Stefan Seemayer, Markus Gruber, Johannes Söding
2014 Computer applications in the biosciences : CABIOS  
Motivation: Recent breakthroughs in protein residue-residue contact prediction have made reliable de novo prediction of protein structures possible.  ...  This impedes the runtime and large-scale contact prediction for larger protein families, multi-domain proteins and protein-protein interactions.  ...  ACKNOWLEDGEMENT We would like to thank Markus Meier for the distribution over SCOP domain lengths and Jessica Andreani, Susann Vorberg, Markus and Armin Meier for helpful comments and discussions.  ... 
doi:10.1093/bioinformatics/btu500 pmid:25064567 pmcid:PMC4201158 fatcat:bb274zyv3bcmhfqdkk7pu4dlvq

Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations

Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang
2021 Cell Reports Methods  
Structure prediction for proteins lacking homologous templates in the Protein Data Bank (PDB) remains a significant unsolved problem.  ...  protein structure prediction.  ...  This work is supported in part by the NIGMS (GM136422 and S10OD026825), the NIAID (AI134678), and the NSF (IIS1901191, DBI2030790, and MTM2025426).  ... 
doi:10.1016/j.crmeth.2021.100014 pmid:34355210 pmcid:PMC8336924 fatcat:arhhxqtquvhr3o7xnzxbcdnlme

Improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning

Jianfeng Sun, Dmitrij Frishman
2021 Computational and Structural Biotechnology Journal  
Here, we present a novel deep-learning approach, DeepTMInter, for sequence-based prediction of interaction sites in α-helical TM proteins based on their topological, physiochemical, and evolutionary properties  ...  Across the main functional families of human transmembrane proteins, the percentage of amino acid sites predicted to be involved in interactions typically ranges between 10% and 25%, and up to 30% in ion  ...  Acknowledgements We are grateful to Bo Zeng for his helpful advice on MBPred, Stephan Breimann for assistance in using the AAanalysis tool, and Peter Hönigschmid for constructive discussions.  ... 
doi:10.1016/j.csbj.2021.03.005 pmid:33815689 pmcid:PMC7985279 fatcat:zhzkm53qtzhcnnfo27vftbeo3e

Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE)

S. Téletchéa, H. Santuz, S. Léonard, C. Etchebest, Björn Wallner
2019 PLoS ONE  
For a given protein entry, initial data are processed from external portals and enriched by using state-of-the-art bioinformatics methods.  ...  for membrane proteins.  ...  Patrick Mayeux and Emilie-Fleur Gautier for fruitful discussions and their valuable support.  ... 
doi:10.1371/journal.pone.0211043 pmid:30794542 pmcid:PMC6386447 fatcat:jcuyqyndufc3bc3nypn4lcblei

Structure of the Type VI Secretion System Contractile Sheath

Mikhail Kudryashev, Ray Yu-Ruei Wang, Maximilian Brackmann, Sebastian Scherer, Timm Maier, David Baker, Frank DiMaio, Henning Stahlberg, Edward H. Egelman, Marek Basler
2015 Cell  
The sheath subunits, composed of tightly interacting proteins VipA and VipB, assemble into a six-start helix.  ...  The helix is stabilized by a core domain assembled from four b strands donated by one VipA and two VipB molecules. The fold of inner and middle layers is conserved between T6SS and phage sheaths.  ...  We thank Kenneth Goldie and Bill Anderson for expert assistance with cryo-EM and Venkat Dandey for support with software.  ... 
doi:10.1016/j.cell.2015.01.037 pmid:25723169 pmcid:PMC4359589 fatcat:f5e7qgyqingljjaumwvmziijky

Protein Structure Prediction by Recurrent and Convolutional Deep Neural Network Architectures

Jack Hanson, University, My, Kuldip Paliwal
2019
Protein contact maps describe the intra-sequence distance between each residue pairing at a distance cuto , providing key restraints towards the possible conformations of a protein.  ...  The method, called SPOT-Disorder, predicts the per-residue probability of a protein being intrinsically disordered (ie. unstructured, or exible).  ...  Baldi,P. et al. (1999) Exploiting the past and the future in protein secondary structure prediction. Bioinformatics, 15, 937-946. Berman,H.M. et al. (2000) The protein data bank.  ... 
doi:10.25904/1912/3830 fatcat:pllucrmcl5cw5nkdvjjpmklgfu