Research Topics
| Anna R PanchenkoSummaryAffiliation: National Institutes of Health Country: USA Publications
| Collaborators
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Detail Information
Publications
Deciphering protein-protein interactions. Part I. Experimental techniques and databasesBenjamin A Shoemaker
Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States of America
PLoS Comput Biol 3:e42. 2007- Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partnersBenjamin A Shoemaker
Computational Biology Branch, National Center for Biotechnology Information, Bethesda, Maryland, United States of America
PLoS Comput Biol 3:e43. 2007..We discuss the applicability of computational methods to different types of prediction problems and point out limitations common to all of them... - Structural similarity of loops in protein families: toward the understanding of protein evolutionAnna R Panchenko
Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
BMC Evol Biol 5:10. 2005..Structurally aligned protein regions are separated by less conserved loop regions, where sequence and structure locally deviate from each other and do not superimpose well... - Evolutionary plasticity of protein families: coupling between sequence and structure variationAnna R Panchenko
Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
Proteins 61:535-44. 2005..Similar sequence-structure analysis performed for protein loop regions shows that evolutionary plasticity of loop regions is greater than for the protein core... - Analysis of protein homology by assessing the (dis)similarity in protein loop regionsAnna R Panchenko
Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
Proteins 57:539-47. 2004.... - Prediction of functional sites by analysis of sequence and structure conservationAnna R Panchenko
Computational Biology Branch, NCBI, Bldg 38A, Rm 8N805, NIH, Bethesda, MD 20894, USA
Protein Sci 13:884-92. 2004..Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites... - Finding weak similarities between proteins by sequence profile comparisonAnna R Panchenko
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 31:683-9. 2003.... - Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sitesBenjamin A Shoemaker
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 38:D518-24. 2010..IBIS is updated regularly and is freely accessible via http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.html... - MMDB: Entrez's 3D-structure databaseJie Chen
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 31:474-7. 2003..MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html... - Homology inference of protein-protein interactions via conserved binding sitesManoj Tyagi
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS ONE 7:e28896. 2012.... - IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteinsBenjamin A Shoemaker
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
Nucleic Acids Res 40:D834-40. 2012..The IBIS server is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi and updated biweekly... - 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... - Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteinsThomas Madej
Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
BMC Struct Biol 7:23. 2007..Along with these we also consider the "gapped structural alignment score" (GSAS), which was introduced earlier by other researchers... - Knowledge-based annotation of small molecule binding sites in proteinsRatna R Thangudu
National Center for Biotechnology Information, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
BMC Bioinformatics 11:365. 2010..To benefit from the rapidly increasing structural data, it is essential to improve the tools that enable large scale binding site prediction with greater emphasis on their biological validity... 
A structure-based method for protein sequence alignmentMaricel G Kann
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
Bioinformatics 21:1451-6. 2005..ncbi.nih.gov/pub/SALTO/), and has been incorporated to Cn3D structure/alignment viewer. CONTACT: ...- Intrinsic disorder in protein interactions: insights from a comprehensive structural analysisJessica H Fong
National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS Comput Biol 5:e1000316. 2009..The fascinating diversity of roles of disordered regions in various biological processes and protein oligomeric forms shown in our study may be a subject of future endeavors in this area... - CDD: a database of conserved domain alignments with links to domain three-dimensional structureAron Marchler-Bauer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 30:281-3. 2002..CD-Search runs reverse-position-specific BLAST (RPS-BLAST), a variant of the widely used PSI-BLAST algorithm. CD-Search is run by default for protein-protein queries submitted to NCBI's BLAST service at http://www.ncbi.nlm.nih.gov/BLAST... 
Large-scale mapping of human protein interactome using structural complexesManoj Tyagi
National Center for Biotechnology Information, US National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
EMBO Rep 13:266-71. 2012..Moreover, structurally inferred and high-confidence HTP networks complement each other well, allowing us to construct a merged network to generate testable hypotheses and provide valuable experimental leads...- Finding biologically relevant protein domain interactions: conserved binding mode analysisBenjamin A Shoemaker
Computational Biology Branch, National Center for Biotechnology Information, Building 38A, National Institutes of Health, Bethesda, MD 20894, USA
Protein Sci 15:352-61. 2006..The method's ability to sort through and classify large numbers of putative interacting domain pairs is demonstrated on the oligomeric interactions of globins... - Exploring functional roles of multibinding protein interfacesManoj Tyagi
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
Protein Sci 18:1674-83. 2009.... - CDD: a curated Entrez database of conserved domain alignmentsAron Marchler-Bauer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 31:383-7. 2003..This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members... - Modeling the evolution of protein domain architectures using maximum parsimonyJessica H Fong
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
J Mol Biol 366:307-15. 2007..Domain architecture "neighbors" identified in this way may lead to new insights about the evolution of protein function... - Comparison of sequence and structure alignments for protein domainsAron Marchler-Bauer
Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
Proteins 48:439-46. 2002..These observations suggest that structure comparison results might be used to improve the overall accuracy of domain alignment collections and the performance of profile search methods based on them... - 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... - MMDB: 3D structures and macromolecular interactionsThomas Madej
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 40:D461-4. 2012..MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure... - Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerizationKosuke Hashimoto
National Center for Biotechnology Information, National Library of Medicine, National Institutes ofHealth, Bethesda, MD 20894, USA
Phys Biol 8:035007. 2011..Finally, we discuss the possible role of oligomeric transitions in the regulation of protein activity and compile a set of experimental examples with such regulatory mechanisms... - 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... - 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... - Modulating protein-protein interactions with small molecules: the importance of binding hotspotsRatna Rajesh Thangudu
National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
J Mol Biol 415:443-53. 2012..We investigate possible mechanisms of how small molecules may modulate protein-protein binding and discuss examples of new candidates for drug design... - Long-term trends in evolution of indels in protein sequencesYuri Wolf
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
BMC Evol Biol 7:19. 2007..We studied relatively early evolutionary events and focused on protein domains which are conserved among various taxonomy groups... - Functional states of homooligomers: insights from the evolution of glycosyltransferasesKosuke Hashimoto
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Building 38A 8S814, Bethesda, MD 20894, USA
J Mol Biol 399:196-206. 2010.... - A comparison of position-specific score matrices based on sequence and structure alignmentsAnna R Panchenko
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
Protein Sci 11:361-70. 2002..We discuss these observations, and suggest a strategy for constructing seed alignments that optimize PSSM-sequence alignment accuracy and recognition sensitivity... - MMDB: Entrez's 3D-structure databaseYanli Wang
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 30:249-52. 2002..MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure... - Phosphorylation in protein-protein binding: effect on stability and functionHafumi Nishi
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
Structure 19:1807-15. 2011..We discuss the cases where phosphorylation mediates the complex formation and regulates the function. We show that phosphorylation sites are more likely to be evolutionary conserved than other interfacial residues... - Intrinsic protein disorder in human pathwaysJessica H Fong
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Mol Biosyst 8:320-6. 2012..Finally we find that relations involving protein activation and to some extent inhibition are characterized by low disorder content... - 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.... - 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... - 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... - Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric statesKosuke Hashimoto
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Proc Natl Acad Sci U S A 107:20352-7. 2010..Last, we show how the presence or absence of insertions and deletions on interfaces might be of practical value in annotating protein oligomeric states... - The relationship of protein conservation and sequence lengthDavid J Lipman
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
BMC Evol Biol 2:20. 2002..However, additional evolutionary forces that affect the length of a protein may be revealed by studying the length distributions of proteins evolving under weaker functional constraints... - Intrinsic disorder and protein multibinding in domain, terminal, and linker regionsJessica H Fong
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Mol Biosyst 6:1821-8. 2010..In particular, they support the hypothesis that protein domains with many interacting partners should have a pleiotropic effect on functional pathways and consequently might be more constrained in evolution... - 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/... - Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinasesKosuke Hashimoto
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
Hum Mutat 33:1566-75. 2012..The activation mechanisms of double mutations differ from those of single mutations and double mutation spectrum is found to be dissimilar to the mutation spectrum of singletons...