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Combining specificity determining and conserved residues improves functional site prediction

Olga V Kalinina, Mikhail S Gelfand, Robert B Russell
2009 BMC Bioinformatics  
that the addition of SDPs significantly improves functional site prediction accuracy.  ...  Results: Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity.  ...  We combine routine predictions of conserved residues with those for specificity determinants, and use structural information to identify spatial clusters of the predicted important residues.  ... 
doi:10.1186/1471-2105-10-174 pmid:19508719 pmcid:PMC2709924 fatcat:73qqjjagj5aijmsju5xifvqptq

Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction

Elin Teppa, Angela D Wilkins, Morten Nielsen, Cristina Buslje
2012 BMC Bioinformatics  
of specificity determining positions (SDPs): integer-value Evolutionary Trace (ivET), SDPfox, and XDET.  ...  Combined, these observations demonstrate that the rvET and cMI scores add complementary information to the prediction system.  ...  Three clear signals of evolution are: conservation, conservation within specific groups of sequences sharing a common function, and coevolution between residues (see Figure 1 ).  ... 
doi:10.1186/1471-2105-13-235 pmid:22978315 pmcid:PMC3515339 fatcat:qyocpgwvnvb6zkjnb6jarsey4i

Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification

Cristina Marino Buslje, Elin Teppa, Tomas Di Doménico, José María Delfino, Morten Nielsen, Burkhard Rost
2010 PLoS Computational Biology  
A catalytic likeliness score (Cls), combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy.  ...  CR are, in general, conserved and located in the functional site of a protein in order to attain their function.  ...  Conservation is the natural and intuitive way to predict functional residues in proteins.  ... 
doi:10.1371/journal.pcbi.1000978 pmid:21079665 pmcid:PMC2973806 fatcat:7cgy5khgpvfz5ie6haxs2ftyyu

Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design

G. Cheng
2005 Nucleic Acids Research  
The combined sequence and structure based functional site prediction method has been implemented in a publicly available web server.  ...  with sub-optimal free energies, and that incorporation of these two measures improves sequence based prediction of protein functional sites.  ...  We thank Michal Guerquin and Keith Laidig for efficient computer cluster management. This work was supported by Searle Scholar Award, NSF Grant DBI-0217241, NIH Grant GM068152 to (RS).  ... 
doi:10.1093/nar/gki894 pmid:16224101 pmcid:PMC1258172 fatcat:f7csxqkn65dipjl6jrddqomohy

CATH functional families predict functional sites in proteins

Sayoni Das, Harry M Scholes, Neeladri Sen, Christine Orengo, Arne Elofsson
2020 Bioinformatics  
We show that conserved residues in FunFams are enriched in functional sites.  ...  Several methods are available for predicting either a generic functional site, or specific types of functional site.  ...  Jonathan Lees and Dr. Ian Sillitoe for their helpful advice on various aspects of this work. Funding  ... 
doi:10.1093/bioinformatics/btaa937 pmid:33135053 pmcid:PMC8150129 fatcat:oojbgj25g5cm7b5z3qlz6aeysq

Automatic Methods for Predicting Functionally Important Residues

Antonio del Sol Mesa, Florencio Pazos, Alfonso Valencia
2003 Journal of Molecular Biology  
the same time which exhibit the specificity of each subfamily ("Tree-determinant residues").  ...  Sequence analysis is often the first guide for the prediction of residues in a protein family that may have functional significance.  ...  Garcia-Ranea into the predictions of the ras binding sites. A. del Sol developed the S-method and F. Pazos the MB and SS-methods. Both of them carried out the analysis of the results. A.  ... 
doi:10.1016/s0022-2836(02)01451-1 pmid:12589769 fatcat:qkepu54vwbeblkgpaewojkdewm

Evolutionary coupling analysis identifies the impact of disease-associated variants at less-conserved sites

2019 Nucleic Acids Research  
Current methods to predict the mutational impacts depend on evolutionary conservation at the mutation site, which is determined using homologous sequences and based on the assumption that variants at well-conserved  ...  However, many DVs at less-conserved but functionally important sites cannot be predicted by the current methods.  ...  Authors' Contributions: D.K. and S.K. conceived and designed the experiments. D.K. and K.L. performed the experiments. D.K., S.K.H. and S.K. analyzed the data.  ... 
doi:10.1093/nar/gkz536 pmid:31199866 pmcid:PMC6895274 fatcat:kkxk7t44izfptoq4sutejof25y

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

Taner Z Sen, Andrzej Kloczkowski, Robert L Jernigan, Changhui Yan, Vasant Honavar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs
2004 BMC Bioinformatics  
We developed a consensus method for predicting protein-protein interface residues by combining sequence and structure-based methods.  ...  Identification of protein-protein interaction sites and detection of specific amino acids that contribute to the specificity and the strength of protein interactions is an important problem with broad  ...  Dobbs and R.L. Jernigan. We thank Dimitris Margaritis and other members of our research groups for helpful discussions.  ... 
doi:10.1186/1471-2105-5-205 pmid:15606919 pmcid:PMC544855 fatcat:423hjz622jhhhfaugjxbhyed4a

CATH functional families predict protein functional sites [article]

Sayoni Das, Harry M. Scholes, Christine A. Orengo
2020 bioRxiv   pre-print
FunSite outperformed all publicly-available functional site prediction methods. We show that conserved residues in FunFams are enriched in functional sites.  ...  Several methods are available for predicting either a generic functional site, or specific types of functional site.  ...  Jonathan Lees and Dr. Ian Sillitoe for their helpful advice on various aspects of this work. Funding  ... 
doi:10.1101/2020.03.23.003012 fatcat:ishjyeqedjhobdbh4emgqtcaru

Characterization and prediction of residues determining protein functional specificity

John A. Capra, Mona Singh
2008 Computer applications in the biosciences : CABIOS  
Knowledge of these specificity determining positions (SDPs) aids in protein function prediction, drug design and experimental analysis.  ...  Often, the amino acids present in a small number of sequence positions determine each protein's particular functional specificity.  ...  M.S. thanks the NSF for grants IIS-0612231 and PECASE MCB-0093399, and the NIH for grant GM076275.  ... 
doi:10.1093/bioinformatics/btn214 pmid:18450811 pmcid:PMC2718669 fatcat:xsfllb757jfknmidomeouxxl5m

INTREPID—INformation-theoretic TREe traversal for Protein functional site IDentification

Sriram Sankararaman, Kimmen Sjölander
2008 Computer applications in the biosciences : CABIOS  
We evaluated INTREPID on two tasks: predicting catalytic residues and predicting specificity determinants.  ...  In particular, INTREPID is able to better predict catalytic positions that are not globally conserved and hence, attains improved sensitivity at high values of specificity.  ...  The authors would also like to thank Anthony Capra and Mona Singh for the SDP dataset and the GroupSim code, and Eunseog Youn and Sean Mooney for access to their dataset.  ... 
doi:10.1093/bioinformatics/btn474 pmid:18776193 pmcid:PMC2572704 fatcat:gcxnihd5yjdz5hfwtaiih7klvy

Structure-based Markov random field model for representing evolutionary constraints on functional sites

Chan-Seok Jeong, Dongsup Kim
2016 BMC Bioinformatics  
This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information.  ...  Results: In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the  ...  Acknowledgements We thank all of the members of the Bioinformatics and Computational Biology Laboratory (BCBL) for helpful discussion.  ... 
doi:10.1186/s12859-016-0948-2 pmid:26911566 pmcid:PMC4765150 fatcat:h4x4qnhqu5cenjsmlq7oo2l44y

CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data

Jan-Oliver Janda, Andreas Meier, Rainer Merkl
2013 Computer applications in the biosciences : CABIOS  
Motivation: The precise identification of functionally and structurally important residues of a protein is still an open problem, and state-ofthe-art classifiers predict only one or at most two different  ...  A comparison with existing methods confirmed stateof-the-art prediction quality, even though CLIPS-4D classifies more specifically than other methods.  ...  in the vicinity of residue k and has been reported as improving the prediction of catalytic sites (Buslje et al., 2010) .  ... 
doi:10.1093/bioinformatics/btt519 pmid:24048358 fatcat:d5ez4ym7cnbonnxnhwfzlqvycy

Improving position-specific predictions of protein functional sites using phylogenetic motifs

K. C. Dukka Bahadur, Dennis R. Livesay
2008 Computer applications in the biosciences : CABIOS  
Using phylogenetic motifs (PMs), we have developed two combined (conservation + PMs) prediction schemes that significantly improve prediction accuracy.  ...  Motivation: Accurate computational prediction of protein functional sites is critical to maximizing the utility of recent high-throughput sequencing efforts.  ...  Valdar for providing Scorecons, Dr Florencio Pazos for providing Xdet and Dr Jonathan R. Manning and Dr Geoff J. Barton for assisting us with SMERFS.  ... 
doi:10.1093/bioinformatics/btn454 pmid:18723520 fatcat:vic46se5sbfodm3dfnuctl2ese

Functional Specificity Lies within the Properties and Evolutionary Changes of Amino Acids

Saikat Chakrabarti, Stephen H. Bryant, Anna R. Panchenko
2007 Journal of Molecular Biology  
To address this critical problem we developed a method named SPEER (specificity prediction using amino acids' properties, entropy and evolution rate) to distinguish specificity determining sites from others  ...  The rapid increase in the amount of protein sequence data has created a need for automated identification of sites that determine functional specificity among related subfamilies of proteins.  ...  Acknowledgements We thank Michael Galperin and Oishee Chakrabarti for helpful discussions and Thomas Madej for critically reading the manuscript.  ... 
doi:10.1016/j.jmb.2007.08.036 pmid:17868687 pmcid:PMC2605514 fatcat:v2swuiec55cfnguxm5vlpevyhi
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