Publications

2019

2018

2017

2016

2015

2014

2013

2012 and before

  • Kosuke Hashimoto, Igor B. Rogozin and Anna R. Panchenko Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases, Hum Mutat (2012).
  • Chakraborty A, Mandloi S, Lanczycki CJ, Panchenko AR, Chakrabarti S SPEER-SERVER: a web server for prediction of protein specificity determining sites, Nucleic Acids Res (2012).
  • Sayers EW et al. Database resources of the National Center for Biotechnology Information, Nucleic Acids Res (2012).
  • Benjamin A. Shoemaker , Dachuan Zhang, Manoj Tyagi, Rajesh R. Thangudu , Jessica H. Fong , Aron Marchler-Bauer , Stephen H. Bryant , Thomas Madej and Anna R. Panchenko IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins, Nucleic Acids Res (2012).
  • Thomas Madej, Kenneth J. Addess, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Christopher J. Lanczycki, Chunlei Liu, Shennan Lu, Aron Marchler-Bauer, Anna R. Panchenko, Jie Chen, Paul A. Thiessen, Yanli Wang, Dachuan Zhang and Stephen H. Bryant MMDB: 3D structures and macromolecular interactions, Nucleic Acids Res (2012).
  • Manoj Tyagi, Kosuke Hashimoto, Benjamin Shoemaker, Stefan Wuchty and Anna R. Panchenko Large-scale mapping of human protein interactome using structural complexes, EMBO Reports (2012).
  • Manoj Tyagi, Ratna Thangudu, Dachuan Zhang, Stephen Bryant, Thomas Madej and Anna R. Panchenko Homology Inference of Protein-Protein Interactions via Conserved Binding Sites, Plos One (2012).
  • Ratna R Thangudu, Stephen Bryant; Anna R Panchenko and Thomas Madej Modulating protein-protein interactions with small molecules: the importance of binding hotspots, J Mol Biol (2012).
  • Jessica H. Fong, Benjamin A. Shoemaker and Anna R. Panchenko Intrinsic protein disorder in human pathways, Mol Biosyst (2012).
  • Hafumi Nishi, Kosuke Hashimoto and Anna R. Panchenko Phosphorylation in protein-protein binding: effect on stability and function, Structure (2011).
  • Kosuke Hashimoto, Hafumi Nishi, Stephen Bryant and Anna R. Panchenko Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization, Phys Biol (2011).
  • Ruth Nussinov, Anna R. Panchenko and Teresa Przytycka Physics approaches to protein interactions and gene regulation, Phys Biol (2011).
  • Sayers EW et al. Database resources of the National Center for Biotechnology Information, Nucleic Acids Res (2011).
  • Inbar Cohen-Gihon, Jessica H. Fong, Roded Sharan, Ruth Nussinov, Teresa Przytycka and Anna R. Panchenko Evolution of domain promiscuity in eukaryotic genomes-a perspective from the inferred ancestral domain architectures, Mol Biosys (2010).
  • Kosuke Hashimoto and Anna R. Panchenko Mechanisms of protein oligomerization: the critical role of insertions and deletions in maintaining different oligomeric states, Proc Natl Acad Sci (2010).
  • Ratna Thangudu, Manoj Tyagi, Benjamin Shoemaker, Stephen Bryant, Anna R. Panchenko and Thomas Madej Knowledge-based annotation of small molecule binding sites in proteins, BMC Bioinformatics (2010).
  • Jessica Fong and Anna R. Panchenko "Intrinsic disorder and protein multibinding in domain, terminal, and linker regions", Mol Biosys, Oct 1;6(10):1821-8 (2010).
  • Kosuke Hashimoto, Thomas Madej, Stephen Bryant and Anna R. Panchenko "Functional states of homooligomers: insights from the evolution of glycosyltransferases" J Mol Biol., 399(1):196-206 (2010).
  • Saikat Chakrabarti and Anna R. Panchenko "Structural and functional roles of coevolved sites in proteins", PloS One, Jan 6;5(1):e8591 (2010).
  • Sayers EW et al. "Database resources of the National Center for Biotechnology Information", Nucleic Acids Res, D5-16 (2010).
  • Judith E. Dayhoff, Benjamin A. Shoemaker, Stephen Bryant and Anna R. Panchenko "Evolution of protein binding modes in homooligomers", J Mol Biol, v. 395(4), p. 860 (2010).
  • Michael Lobanov, Benjamin A. Shoemaker,Sergei O. Garbuzynskiy, Jessica H. Fong, Anna R. Panchenko and Oxana V. Galzitskaya "ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder", Nucleic Acids Res., D283-7 (2010).
  • Benjamin A. Shoemaker, Dachuan Zhang, Ratna R. Thangudu, Manoj Tyagi, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Thomas Madej and Anna R. Panchenko "Inferred Biomolecular Interaction Server (IBIS) a web server to analyze and predict protein interacting partners and binding sites", Nucleic Acids Res. D518-24 (2010).
  • Manoj Tyagi, Benjamin A. Shoemaker, Stephen Bryant and Anna R. Panchenko "Exploring functional roles of multibinding protein interfaces", Protein Science, v. 18(8), p.1674 (2009).
  • S. Teng S, Thomas Madej, Anna R. Panchenko and Emil Alexov "Modeling effects of human single nucleotide polymorphisms on protein-protein interactions", Biophys J, v.96(11) (2009).
  • Saikat Chakrabarti and Anna R. Panchenko "Ensemble approach to predict specificity determinants: benchmarking and validation", BMC Bioinformatics, 10:207 (2009).
  • Jessica H. Fong, Benjamin A. Shoemaker, Sergey O. Garbuzynskiy, Michael Y. Lobanov, Oxana V. Galzitskaya and Anna R. Panchenko "Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis", PLoS Comput Biol, v.5(3) (2009).
  • Maricel G. Kann MG, Benjamin A. Shoemaker, Anna R. Panchenko and Teresa M. Przytycka "Correlated evolution of interacting proteins: looking behind the mirrortree", J Mol Biol, v.385, p.91 (2009).
  • Saikat Chakrabarti and Anna R. Panchenko "Coevolution in defining the functional specificity", Proteins, v.75, p.231 (2009).
  • Saikat Chakrabarti, Stephen Bryant and Anna R. Panchenko "Functional specificity lies within the properties and evolutionary changes of amino acids", J Mol Biol, v.373(3), p.801 (2007).
  • Benjamin A. Shoemaker and Anna R. Panchenko "Deciphering protein- protein interactions. I. Experimental techniques and databases", PLoS Comput Biol, v. 3(4) (2007).
  • Thomas Madej, Anna R. Panchenko, Jie Chen and Stephen Bryant "Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins", BMC Struct Biol, v 7:23 (2007).
  • Benjamin A. Shoemaker and Anna R. Panchenko "Deciphering protein-protein interactions. II. Computational methods to predict protein and domain interaction partners", PLoS Comput Biol, v. 3(3) (2007).
  • Yuri Wolf, Thomas Madej, Vladimir Babenko, Benjamin Shoemaker and Anna R. Panchenko "Long-term trends in evolution of indels in protein sequences", BMC Evol. Biol., v.7:19 (2007).
  • Jessica Fong, Lewis Geer, Anna R. Panchenko and Stephen H. Bryant "Modeling the evolution of protein domain architectures using maximum parsimony", J. Mol. Biol., v. 366(1), p.307 (2007).
  • Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen and Stephen H. Bryant "State of the art: refinement of multiple sequence alignments", BMC Bioinfomatics,14,7:499 (2006).
  • Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen and Stephen H. Bryant "Refining multiple sequence alignments with conserved core regions", Nucleic Acids Res., v.34(9), p.2598 (2006).
  • Benjamin A. Shoemaker, Anna R. Panchenko and Stephen H. BryantFinding biologically relevant domain interactions: Conserved Binding Mode analysis, Protein Science, v.15(2), p.352 (2006).
  • Anna R. Panchenko, Yuri I. Wolf, Larisa Panchenko and Thomas MadejEvolutionary plasticity of protein families: coupling between sequence and structure variation, Proteins, v.61, p. 535 (2005).
  • Anna R. Panchenko and Thomas Madej Structural similarity of loops in protein families: toward the understanding of protein evolution, BMC Evolutionary Biology, 5(1), p.10 (2005).
  • Maricel Kann, Paul Thiessen, Anna R. Panchenko, Alejandro Schaffer, Stephen Altschul and Stephen BryantA Structure-based Method for Protein Sequence Alignment, Bioinformatics, v. 21(8), p.1451 (2005).
  • Anna R. Panchenko and Thomas Madej Analysis of protein homology by assessing the (dis)similarity in protein loop regions, Proteins, v.57(3), p.539(2004).
  • Anna R. Panchenko, Fyodor Kondrashov and Stephen BryantPrediction of functional sites by analysis of sequence and structure conservation, Protein Science, v.13, p. 884-892 (2004).
  • Anna R. Panchenko Finding weak protein similarities by sequence profile comparison, Nucleic Acids Res., v. 31(2), p.683-689 (2003).
  • Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin and Stephen H. BryantMMDB: Entrezs 3D-structure database, Nucleic Acids Res., v. 31(1), p. 474-477 (2003).
  • Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin and Stephen H. BryantCDD: a curated Entrez database of conserved domain alignments, Nucleic Acids Res., v.31(1), p. 383-387 (2003).
  • David Lipman, Alexander Souvorov, Eugene Koonin, Anna R. Panchenko and Tatyana TatusovaThe relationship of protein conservation and sequence length, BMC Evol Biol, Nov 1;2(1):20 (2002).
  • Aron Marcheler-Bauer, Anna R. Panchenko, Naomi Ariel and Stephen BryantComparison of sequence and structure alignments for protein domains, Proteins, v.48(3), p.439-446 (2002).
  • Anna R. Panchenko and Stephen Bryant A comparison of Position-Specific Score Matrices based on sequence and structure alignments, Protein Science, v. 11, p. 361-370 (2002).
  • Yanli Wang, John B. Anderson, Jie Chen, Lewis Y. Geer, Siqian He, David I. Hurwitz, Cynthia A. Liebert, Thomas Madej, Gabriele H. Marchler, Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Stephen H. Bryant
    MMDB: Entrezs 3D-Structure Database, Nucleic Acids Res., v. 30(1), p.281-283 (2002).
  • Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, Paul A.Thiessen, Lewis Y. Geer and Stephen H. BryantCDD: A Database of Conserved Domain Alignments with links to domain three- dimensional structure, Nucleic Acids Res., v. 30(1), p. 249-252 (2002).
  • Anna R. Panchenko, Aron Marchler-Bauer and Stephen H. BryantCombination of threading potentials and sequence profiles improves fold- recognition, J. of Mol. Biol., v.296, p. 1319-1331 (2000).
  • Anna R. Panchenko, Aron Marchler-Bauer and Stephen H. BryantThreading with explicit models for evolutionary conservation of structure and sequence, Proteins, v. 3, p. 133-141 (1999).
  • Anna R. Panchenko, Zaida Luthey-Schulten, Roland Cole and Peter G. Wolynes
    The foldon universe: a survey of structural similarity and self-recognition of independently folding units, J. of Mol. Biol., v. 272, p. 95-105 (1997).
  • Anna R. Panchenko, Zaida Luthey-Schulten and Peter G. WolynesFoldons as independently folding units of proteins, Physica D, v. 107, p. 312-315 (1997).
  • Anna R. Panchenko, Zaida Luthey-Schulten and Peter G. WolynesFoldons, protein structural modules and exons, Proc. Natl. Acad. Sci., v. 93, p. 2008-2013 (1996).
  • Anna R. Panchenko, Jing Wang, G. Ulrich Nienhaus and Peter G. WolynesAnalysis of ligand binding to heme proteins using a fluctuating path description, J. of Phys. Chem., v. 99, p. 9278-9282 (1995).
  • Anna R. Panchenko and K. V. Shaitan Effect of pressure on intramolecular dynamics of proteins, Molecular Biology, v. 26, p. 745-748 (1992).
  • Anna R. Panchenko and K. V. Shaitan Effect of dynamic disorder of biological systems on the characteristics of intramolecular mobility determined by Mossbauer spectroscopy, Biophysics, v. 37, p. 927-931 (1992).