Anna R Panchenko

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Deciphering protein-protein interactions. Part I. Experimental techniques and databases
    Benjamin 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
  2. pmc Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
    Benjamin A Shoemaker
    Computational Biology Branch, National Center for Biotechnology Information, Bethesda, Maryland, United States of America
    PLoS Comput Biol 3:e43. 2007
  3. pmc Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites
    Benjamin 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
  4. pmc Cancer missense mutations alter binding properties of proteins and their interaction networks
    Hafumi Nishi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 8:e66273. 2013
  5. pmc IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
    Benjamin 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
  6. pmc Large-scale mapping of human protein interactome using structural complexes
    Manoj 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
  7. ncbi request reprint Seasonal variations in rat resistance to hypoxia
    M L Khachatur'yan
    Department of Experimental Laboratory Models, Russian State Medical University
    Bull Exp Biol Med 133:300-3. 2002
  8. pmc Structural similarity of loops in protein families: toward the understanding of protein evolution
    Anna R Panchenko
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 5:10. 2005
  9. pmc Analysis of protein homology by assessing the (dis)similarity in protein loop regions
    Anna R Panchenko
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 57:539-47. 2004
  10. pmc Prediction of functional sites by analysis of sequence and structure conservation
    Anna R Panchenko
    Computational Biology Branch, NCBI, Bldg 38A, Rm 8N805, NIH, Bethesda, MD 20894, USA
    Protein Sci 13:884-92. 2004

Detail Information

Publications49

  1. pmc Deciphering protein-protein interactions. Part I. Experimental techniques and databases
    Benjamin 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
  2. pmc Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
    Benjamin 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...
  3. pmc Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites
    Benjamin 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...
  4. pmc Cancer missense mutations alter binding properties of proteins and their interaction networks
    Hafumi Nishi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 8:e66273. 2013
    ..Such observations suggest that genes with mutations directly affecting protein binding properties are preferably located in central network positions and may influence critical nodes and edges in signal transduction networks. ..
  5. pmc IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
    Benjamin 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...
  6. pmc Large-scale mapping of human protein interactome using structural complexes
    Manoj 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...
  7. ncbi request reprint Seasonal variations in rat resistance to hypoxia
    M L Khachatur'yan
    Department of Experimental Laboratory Models, Russian State Medical University
    Bull Exp Biol Med 133:300-3. 2002
    ..Fluctuations in the life span during the day and year were more expressed in low- and medium-resistant rats. Differences in the life span of highly and low-resistant rats were the most pronounced in winter...
  8. pmc Structural similarity of loops in protein families: toward the understanding of protein evolution
    Anna 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...
  9. pmc Analysis of protein homology by assessing the (dis)similarity in protein loop regions
    Anna R Panchenko
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 57:539-47. 2004
    ....
  10. pmc Prediction of functional sites by analysis of sequence and structure conservation
    Anna 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...
  11. pmc Finding weak similarities between proteins by sequence profile comparison
    Anna 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
    ....
  12. pmc Evolutionary plasticity of protein families: coupling between sequence and structure variation
    Anna 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...
  13. pmc MMDB: Entrez's 3D-structure database
    Jie 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...
  14. pmc Homology inference of protein-protein interactions via conserved binding sites
    Manoj 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
    ....
  15. pmc Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins
    Thomas 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...
  16. 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...
  17. pmc Knowledge-based annotation of small molecule binding sites in proteins
    Ratna 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...
  18. ncbi request reprint A structure-based method for protein sequence alignment
    Maricel 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
    ....
  19. pmc Finding biologically relevant protein domain interactions: conserved binding mode analysis
    Benjamin 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...
  20. pmc CDD: a database of conserved domain alignments with links to domain three-dimensional structure
    Aron 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...
  21. pmc Exploring functional roles of multibinding protein interfaces
    Manoj 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
    ....
  22. pmc Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis
    Jessica 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...
  23. pmc MMDB: Entrez's 3D-structure database
    Yanli 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...
  24. pmc Modeling the evolution of protein domain architectures using maximum parsimony
    Jessica 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...
  25. pmc CDD: a curated Entrez database of conserved domain alignments
    Aron 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...
  26. pmc Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization
    Kosuke 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...
  27. pmc Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes
    Hafumi Nishi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biosyst 9:1620-6. 2013
    ..We analyze possible mechanisms of how phosphorylation might regulate protein-protein binding via intrinsic disorder, and specifically focus on how phosphorylation could prevent disorder-order transitions upon binding...
  28. ncbi request reprint Comparison of sequence and structure alignments for protein domains
    Aron 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...
  29. 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...
  30. pmc A comparison of position-specific score matrices based on sequence and structure alignments
    Anna 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...
  31. pmc Functional states of homooligomers: insights from the evolution of glycosyltransferases
    Kosuke 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
    ....
  32. 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...
  33. 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...
  34. pmc MMDB: 3D structures and macromolecular interactions
    Thomas 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...
  35. pmc Modulating protein-protein interactions with small molecules: the importance of binding hotspots
    Ratna 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...
  36. pmc Long-term trends in evolution of indels in protein sequences
    Yuri 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...
  37. pmc Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics
    Minghui Li
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
    J Phys Chem B 117:13226-34. 2013
    ..Therefore, the reduced nuclear-cytoplasm ratio of NFAT5 can be attributed to reduced binding to DNA for the triple mutant, while the T222D mutant suggests an additional mechanism at work. ..
  38. pmc Phosphorylation in protein-protein binding: effect on stability and function
    Hafumi 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...
  39. pmc Intrinsic protein disorder in human pathways
    Jessica 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...
  40. 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...
  41. 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
    ....
  42. 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...
  43. pmc Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization
    Hafumi Nishi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Prog Mol Biol Transl Sci 117:3-24. 2013
    ..In this chapter, we summarize the biological importance of homooligomeric assemblies, physicochemical properties of their interfaces, experimental methods for their identification, their evolution, and role in human diseases...
  44. pmc Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states
    Kosuke 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...
  45. pmc The relationship of protein conservation and sequence length
    David 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...
  46. pmc Intrinsic disorder and protein multibinding in domain, terminal, and linker regions
    Jessica 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...
  47. pmc Computational large-scale mapping of protein-protein interactions using structural complexes
    Benjamin Shoemaker
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland
    Curr Protoc Protein Sci 73:3.9.1-9. 2013
    ..Curr. Protoc. Protein Sci. 73:3.9.1-3.9.9. © 2013 by John Wiley & Sons, Inc. ..
  48. 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/...
  49. pmc Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases
    Kosuke 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...