Saikat Chakrabarti

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Analysis and prediction of functionally important sites in proteins
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Libary of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Protein Sci 16:4-13. 2007
  2. pmc Structural and functional roles of coevolved sites in proteins
    Saikat 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
  3. pmc Ensemble approach to predict specificity determinants: benchmarking and validation
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    BMC Bioinformatics 10:207. 2009
  4. pmc Coevolution in defining the functional specificity
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 75:231-40. 2009
  5. pmc Functional specificity lies within the properties and evolutionary changes of amino acids
    Saikat 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
  6. pmc State of the art: refinement of multiple sequence alignments
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 7:499. 2006
  7. pmc Refining multiple sequence alignments with conserved core regions
    Saikat 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
  8. ncbi request reprint State of the art: refinement of multiple sequence alignments
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 11:3. 2010
  9. pmc SPEER-SERVER: a web server for prediction of protein specificity determining sites
    Abhijit 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
  10. ncbi request reprint SSToSS--sequence-structural templates of single-member superfamilies
    Saikat Chakrabarti
    National Centre for Biological Sciences, UAS GKVK Campus, Bellary Road, Bangalore 560 065, India
    In Silico Biol 6:311-9. 2006

Collaborators

Detail Information

Publications18

  1. pmc Analysis and prediction of functionally important sites in proteins
    Saikat 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...
  2. pmc Structural and functional roles of coevolved sites in proteins
    Saikat 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
    ....
  3. pmc Ensemble approach to predict specificity determinants: benchmarking and validation
    Saikat 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...
  4. pmc Coevolution in defining the functional specificity
    Saikat 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...
  5. pmc Functional specificity lies within the properties and evolutionary changes of amino acids
    Saikat 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...
  6. pmc State of the art: refinement of multiple sequence alignments
    Saikat 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...
  7. pmc Refining multiple sequence alignments with conserved core regions
    Saikat 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...
  8. ncbi request reprint State of the art: refinement of multiple sequence alignments
    Saikat 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...
  9. pmc SPEER-SERVER: a web server for prediction of protein specificity determining sites
    Abhijit 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/...
  10. ncbi request reprint SSToSS--sequence-structural templates of single-member superfamilies
    Saikat 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...
  11. ncbi request reprint SMotif: a server for structural motifs in proteins
    Ganesan 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...
  12. pmc SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs
    Saikat 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...
  13. pmc MegaMotifBase: a database of structural motifs in protein families and superfamilies
    Ganesan 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...
  14. pmc Improvement of alignment accuracy utilizing sequentially conserved motifs
    Saikat 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...
  15. ncbi request reprint Regions of minimal structural variation among members of protein domain superfamilies: application to remote homology detection and modelling using distant relationships
    Saikat Chakrabarti
    National Centre for Biological Sciences, UAS GKVK Campus, Bellary Road, Bangalore 560 065, India
    FEBS Lett 569:31-6. 2004
    ....
  16. ncbi request reprint Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints
    Saikat 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...
  17. ncbi request reprint SMoS: a database of structural motifs of protein superfamilies
    Saikat 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...
  18. ncbi request reprint Functional sites and evolutionary connections of acylhomoserine lactone synthases
    Saikat 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...