Research Topics | Saikat ChakrabartiSummaryAffiliation: National Institutes of Health Country: USA Publications
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Publications
Analysis and prediction of functionally important sites in proteinsSaikat Chakrabarti
National Center for Biotechnology Information, National Libary of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Protein Sci 16:4-13. 2007..This prediction method is based on information derived from homologous sequences and no structural information is required. Therefore, this method could be extremely useful for large-scale functional annotation...- Structural and functional roles of coevolved sites in proteinsSaikat Chakrabarti
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS ONE 5:e8591. 2010.... - Ensemble approach to predict specificity determinants: benchmarking and validationSaikat Chakrabarti
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
BMC Bioinformatics 10:207. 2009..Subsequently, three best performing methods were applied to identify new potential specificity determining sites through ensemble approach and common agreement of their prediction results... - Coevolution in defining the functional specificitySaikat Chakrabarti
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
Proteins 75:231-40. 2009..Such correlated changes and compensations can be realized through the stepwise coevolutionary processes which in turn can shed light on the mechanisms of functional diversification... - Functional specificity lies within the properties and evolutionary changes of amino acidsSaikat Chakrabarti
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
J Mol Biol 373:801-10. 2007..Extensive benchmarking by comparing the performance of SPEER with other specificity site prediction algorithms has shown that it performs better in predicting several categories of subfamily specific sites... - State of the art: refinement of multiple sequence alignmentsSaikat Chakrabarti
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
BMC Bioinformatics 7:499. 2006..Refinement of existing alignment can prove to be an intelligent choice considering the increasing importance of high quality alignments in large scale high-throughput analysis... - Refining multiple sequence alignments with conserved core regionsSaikat Chakrabarti
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 34:2598-606. 2006..A standalone version of the program is available by ftp distribution (ftp://ftp.ncbi.nih.gov/pub/REFINER) and will be incorporated into the next release of the Cn3D structure/alignment viewer... 
State of the art: refinement of multiple sequence alignmentsSaikat Chakrabarti
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
BMC Bioinformatics 11:3. 2010..ABSTRACT: Correction to Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA and Bryant SH: State of the art: refinement of multiple sequence alignments. BMC Bioinformatics 2006, 7:499...- SPEER-SERVER: a web server for prediction of protein specificity determining sitesAbhijit Chakraborty
Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research CSIR Indian Institute of Chemical Biology IICB, Kolkata, West Bengal 700032, India
Nucleic Acids Res 40:W242-8. 2012..Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/... - SSToSS--sequence-structural templates of single-member superfamiliesSaikat Chakrabarti
National Centre for Biological Sciences, UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India
In Silico Biol 6:311-9. 2006..This enables the inclusion of singletons to provide added value to the recognition of additional members, comparative modeling and in designing experiments... - SMotif: a server for structural motifs in proteinsGanesan Pugalenthi
School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798
Bioinformatics 23:637-8. 2007..AVAILABILITY: SMotif server is available via the URL http://caps.ncbs.res.in/SMotif/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online... - SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifsSaikat Chakrabarti
National Centre for Biological Sciences (NCBS, Bangalore 560065, India
Nucleic Acids Res 33:W274-6. 2005..The SCANMOT server is available via http://www.ncbs.res.in/~faculty/mini/scanmot/scanmot.html... - MegaMotifBase: a database of structural motifs in protein families and superfamiliesGanesan Pugalenthi
School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
Nucleic Acids Res 36:D218-21. 2008..MegaMotifBase can be a useful resource to gain knowledge about structure and functional relationship of proteins. The database can be accessed from the URL http://caps.ncbs.res.in/MegaMotifbase/index.html... - Improvement of alignment accuracy utilizing sequentially conserved motifsSaikat Chakrabarti
National Centre for Biological Sciences TIFR, Bangalore 560065, India
BMC Bioinformatics 5:167. 2004..In recent times, improvement of existing progressing programs and implementation of new iterative algorithms have made a significant change in this field... - Regions of minimal structural variation among members of protein domain superfamilies: application to remote homology detection and modelling using distant relationshipsSaikat Chakrabarti
National Centre for Biological Sciences, UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India
FEBS Lett 569:31-6. 2004.... - Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraintsSaikat Chakrabarti
National Centre for Biological Sciences TIFR, UAS GKVK Campus, Bellary Road, 560065 Bangalore, India
J Mol Model 10:69-75. 2004..We demonstrate the influence of such approaches to homology modeling during distant relationships in understanding functional properties of protein such as ligand binding using cytochrome P450 as an example... - SMoS: a database of structural motifs of protein superfamiliesSaikat Chakrabarti
National Centre for Biological Sciences, Bangalore 560065, India and Centre for Biotechnology, Anna University, Chennai 600025, India
Protein Eng 16:791-3. 2003..These motifs, along with their sequence and spatial orientation, represent the conserved core structure of each superfamily and also provide the minimal requirement of sequence and structural information to retain each superfamily fold... - Functional sites and evolutionary connections of acylhomoserine lactone synthasesSaikat Chakrabarti
National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bangalore 560 065, India
Protein Eng 16:271-8. 2003..Evolutionary trace analyses of aligned sequences and docking studies have been used to discuss functionally important residues of EsaI homologues...