{"id":113,"date":"2013-06-18T14:43:28","date_gmt":"2013-06-18T18:43:28","guid":{"rendered":"https:\/\/www.bu.edu\/bmerc\/?page_id=113"},"modified":"2020-08-19T11:57:00","modified_gmt":"2020-08-19T15:57:00","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.bu.edu\/bmerc\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<h2><b>2020<\/b><\/h2>\n<ul>\n<li><span>Desta IT, Porter KA, Xia B, Kozakov D, Vajda S. (2020). <\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0969212620302094\"><span>Performance and Its Limits in Rigid Body Protein-Protein Docking<\/span><\/a><span>. Structure.<\/span><\/li>\n<li><span>Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, et al.. (2020). <\/span><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/prot.25887\"><span>ClusPro in rounds 38 to 45 of CAPRI: Toward combining template\u2010based methods with free docking<\/span><\/a><span>. Proteins: Structure, Function, and Bioinformatics.<\/span><\/li>\n<li><span>Khramushin A, Marcu O, Alam N, Shimony O, Padhorny D, et al.. (2020). <\/span><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/prot.25871\"><span>Modeling beta\u2010sheet peptide\u2010protein interactions: Rosetta FlexPepDock in CAPRI rounds 38\u201045<\/span><\/a><span>. Proteins: Structure, Function, and Bioinformatics.<\/span><\/li>\n<li style=\"list-style-type: none;\">\n<ul><\/ul>\n<\/li>\n<li><span>Sun Z, Wakefield AE, Kolossvary I, Beglov D, Vajda S. (2020). <\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0969212619303910\"><span>Structure-Based Analysis of Cryptic-Site Opening<\/span><\/a><span>. Structure.<\/span><\/li>\n<li><span>Alekseenko A, Kotelnikov S, Ignatov M, Egbert M, Kholodov, Y et al.. (2020). <\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0022283619307119\"><span>ClusPro LigTBM: Automated Template-Based Small Molecule Docking<\/span><\/a><span>. Journal of Molecular Biology.\u00a0<\/span><\/li>\n<li><span>Zhong M, Lynch A, Muellers SN, Jehle S, Lingqi L et al.. (2020). <a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.biochem.9b00943\">Interaction Energetics and Druggability of the Protein\u2013Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2)<\/a>. Biochemistry.<\/span><\/li>\n<\/ul>\n<h2><b>2019<\/b><\/h2>\n<ul>\n<li><span>Porter KA, Padhorny D, Desta I, Ignatov M, Beglov D et al.. (2019). <\/span><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/prot.25808\"><span>Template\u2010Based Modeling by ClusPro in CASP13 and the Potential for Using Co\u2010evolutionary Information in Docking.<\/span><\/a> <span>Proteins: Structure, Function, and Bioinformatics.<\/span><\/li>\n<li><span>Vajda S, Emili A. (2019).<\/span> <a href=\"https:\/\/science.sciencemag.org\/content\/365\/6449\/120.summary\"><span>Mapping global protein contacts.<\/span><\/a><span> Science.<\/span><\/li>\n<li><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/prot.25808\"><span><\/span><\/a><span>Egbert M, Whitty A, Keseru GM, Vajda S. (2019). <\/span><a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jmedchem.8b01732\"><span>Why some targets benefit from beyond rule of five drugs<\/span><\/a><span>. Journal of Medicinal Chemistry.<\/span><\/li>\n<li><span>Yueh C, Rettenmaier J, Xia B, Hall DR, Alekseenko A et al.. (2019). <\/span><a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jmedchem.9b00089\"><span>Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases.<\/span><\/a><span> Journal of Medicinal Chemistry.<\/span><\/li>\n<li><span>Wakefield AE, Mason JS, Vajda S, Keseru GM. (2019).<\/span><a href=\"https:\/\/www.nature.com\/articles\/s41598-019-42618-8\"> <span>Analysis of tractable allosteric sites in G protein-coupled receptors.<\/span><\/a><span> Nature: Scientific Reports.<\/span><\/li>\n<li><span>Froes TQ, Baldini RL, Vajda S, Castilho MS. (2019).<\/span> <a href=\"https:\/\/europepmc.org\/abstract\/med\/31038064\"><span>Structure-based druggability assessment of anti-virulence targets from Pseudomonas aeruginosa<\/span><\/a><span>. Current Protein &amp; Peptide Science.<\/span><\/li>\n<li><span>Porter KA, Desta I, Kozakov D, Vajda S. (2019). <\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0959440X18300691?via%3Dihub\"><span>What method to use for protein-protein docking?<\/span><\/a><span> Current Opinion in Structural Biology.<\/span><\/li>\n<li><span>Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A et al.. (2019). <\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0969212619300036?via%3Dihub\"><span>Allostery in Its Many Disguises: From Theory to Applications.<\/span><\/a><span> Structure.<\/span><\/li>\n<li><span>Trilles R, Beglov D, Chen Q, He H, Wireman R et al.. (2019).<\/span> <a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jmedchem.8b01529\"><span>Discovery of Macrocyclic Inhibitors of Apurinic\/Apyrimidinic Endonuclease 1.<\/span><\/a><span> Journal of Medicinal Chemistry.<\/span><\/li>\n<li><span>Ignatov M, Liu C, Alekseenko A, Sun Z, Padhorny D et al.. (2019). <\/span><a href=\"https:\/\/link.springer.com\/article\/10.1007%2Fs10822-018-0176-0\"><span>Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge.<\/span><\/a><span> Journal of Computer-Aided Molecular Design.<\/span><\/li>\n<\/ul>\n<h2><b>2018<\/b><\/h2>\n<ul>\n<li><span>Beglov D, Hall DR, Wakefield AE, Luo L, Allen KN et al.. (2018).<\/span> <a href=\"https:\/\/www.pnas.org\/content\/115\/15\/E3416\"><span>Exploring the structural origins of cryptic sites on proteins.<\/span><\/a><span> PNAS. <\/span><span>\u00a0\u00a0\u00a0 <\/span> <span>\u00a0\u00a0\u00a0 <\/span> <span>\u00a0\u00a0\u00a0 <\/span><\/li>\n<li><span>Ignatov M, Kazennov A, Kozakov D. (2018). <\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0022283618301426?via%3Dihub\"><span>ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking.<\/span><\/a><span> Journal of Molecular Biology.<\/span><\/li>\n<li><span>Zarbafian S, Moghadasi M, Roshandelpoor A, Nan F, Li K et al.. (2018). <\/span><a href=\"https:\/\/www.nature.com\/articles\/s41598-018-23982-3\"><span>Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes.<\/span><\/a><span> Scientific Reports.<\/span><span>\u00a0\u00a0\u00a0 <\/span> <span>\u00a0\u00a0\u00a0 <\/span> <span>\u00a0\u00a0\u00a0 <\/span> <span>\u00a0\u00a0\u00a0 <\/span><\/li>\n<li><span>Stasyk OG, Denega IO, Padhorny D, Dmytruk KV, Kozakov D et al.. (2018). <\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1357272518301729?via%3Dihub\"><span>Glucose regulation in the methylotrophic yeast Hansenula (Ogataea) polymorpha is mediated by a putative transceptor Gcr1.<\/span><\/a><span> The International Journal of Biochemistry &amp; Cell Biology.<\/span><span>\u00a0\u00a0\u00a0 <\/span> <span>\u00a0\u00a0\u00a0 <\/span><\/li>\n<li><span>Vajda S, Beglov D, Wakefield AE, Egbert M, Whitty A. (2018). <\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1367593118300589?via%3Dihub\"><span>Cryptic binding sites on proteins: definition, detection, and druggability.<\/span><\/a><span> Current Opinion in Chemical Biology.<\/span><\/li>\n<li><span>Padhorny D, Hall DR, Mirzaei H, Mamonov AB, Moghadasi M et al.. (2018). <\/span><a href=\"https:\/\/link.springer.com\/article\/10.1007%2Fs10822-017-0069-7\"><span>Protein-ligand docking using FFT based sampling: D3R case study.<\/span><\/a><span> Journal of Computer-Aided Molecular Design.<\/span><\/li>\n<\/ul>\n<h2><b>2017<\/b><\/h2>\n<ul>\n<li><span>Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE et al.. (2017).<\/span> <a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/prot.25219\"><span>New additions to the ClusPro server motivated by CAPRI.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics.<\/span><\/li>\n<li><span>Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D et al.. (2017).<\/span> <a href=\"https:\/\/www.nature.com\/articles\/nprot.2016.169\"><span>The ClusPro web server for protein\u2013protein docking.<\/span><\/a><span>\u00a0 Nature Protocols.<\/span><\/li>\n<li><span>Yueh C, Hall DR, Xia B, Padhorny D, Kozakov D, Vajda S. (2017). <\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0022283616304430?via%3Dihub\"><span>ClusPro-DC: Dimer Classification by the Cluspro Server for Protein\u2013Protein Docking.<\/span><\/a><span> Journal of Molecular Biology.<\/span><\/li>\n<li><span>Porter KA, Xia B, Beglov D, Bohnuud T, Alam N et al.. (2017). <\/span><a href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/20\/3299\/3738495\"><span>ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. <\/span><\/a><span>\u00a0Bioinformatics.<\/span><\/li>\n<li><span>Alam N, Goldstein O, Xia B, Porter KA, Kozakov D, Schueler-Furman O et al.. (2017). <\/span><a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1005905\"><span>High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock.<\/span><\/a><span> PLoS Computational Biology.<\/span><\/li>\n<li><span>Bohnuud T, Jones G, Schueler-Furman O, Kozakov D. (2017). <\/span><a href=\"https:\/\/link.springer.com\/protocol\/10.1007%2F978-1-4939-6798-8_2\"><span>Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server.<\/span><\/a><span> Methods in Molecular Biology.<\/span><\/li>\n<\/ul>\n<h2><b>2016<\/b><\/h2>\n<ul>\n<li><span>Padhorny D, Kazennov A, Zerbe BS, Porter KA, Xia B et al.. (2016). <\/span><a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.1603929113\"><span>Protein\u2013protein docking by fast generalized Fourier transforms on 5D rotational manifolds.<\/span><\/a><span> Proceedings of the National Academy of Sciences.<\/span><\/li>\n<li><span>Bohnuud T, Luo L, Wodak SJ, Bonvin AMJJ, Weng Z et al.. (2016). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.25063\"><span>A benchmark testing ground for integrating homology modeling and protein docking.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics.<\/span><\/li>\n<li><span>Whitty A, Zhong M, Viarengo L, Beglov D, Hall DR, Vajda S. (2016). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.drudis.2016.02.005\"><span>Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs.<\/span><\/a><span> Drug Discovery Today.<\/span><\/li>\n<li><span>Mamonov AB, Moghadasi M, Mirzaei H, Zarbafian S, Grove LE et al.. (2016). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/jcc.24273\"><span>Focused grid-based resampling for protein docking and mapping.<\/span><\/a><span> Journal of Computational Chemistry.<\/span><\/li>\n<li><span>Xia B, Vajda S, Kozakov D. (2016). <\/span><a href=\"http:\/\/doi.org\/10.1093\/bioinformatics\/btw306\"><span>Accounting for pairwise distance restraints in FFT-based protein\u2013protein docking.<\/span><\/a><span> Bioinformatics.<\/span><span>\u00a0\u00a0\u00a0 <\/span> <span>\u00a0\u00a0\u00a0 <\/span> <span>\u00a0\u00a0\u00a0 <\/span> <span>\u00a0\u00a0\u00a0 <\/span><\/li>\n<li><span>Lensink MF, Velankar S, Kryshtafovych A, Huang S-Y, Schneidman-Duhovny D et al.. (2016). <\/span><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/prot.25007\"><span>Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics.<\/span><\/li>\n<li><span>Im W, Liang J, Olson A, Zhou H-X, Vajda S, Vakser IA. (2016). <\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0022283616301930?via%3Dihub\"><span>Challenges in structural approaches to cell modeling.<\/span><\/a><span> Journal of Molecular Biology.<\/span><\/li>\n<\/ul>\n<h2><b>2015<\/b><\/h2>\n<ul>\n<li><span>Vajda S, Whitty A, Kozakov D. (2015). <\/span><a href=\"http:\/\/www.impactjournals.com\/oncotarget\/index.php?journal=oncotarget&amp;page=article&amp;op=view&amp;path%5B%5D=4968\"><span>Fragments and hot spots in drug discovery.<\/span><\/a><span> Oncotarget.<\/span><\/li>\n<li><span>Kozakov D, Grove LE, Hall DR, Bohnuud T, Mottarella SE et al.. (2015). <\/span><a href=\"http:\/\/dx.doi.org\/10.1038\/nprot.2015.043\"><span>The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins.<\/span><\/a><span> Nature Protocols.<\/span><\/li>\n<li><span>Lukose V, Luo L, Kozakov D, Vajda S, Allen KN, Imperiali B. (2015). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/acs.biochem.5b01086\"><span>Conservation and covariance in small bacterial phosphoglycosyltransferases identify the functional catalytic core.<\/span><\/a><span> Biochemistry.\u00a0<\/span><\/li>\n<li><span>Hall DR, Kozakov D, Whitty A, Vajda S. (2015). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.tips.2015.08.003\"><span>Lessons from hot spot analysis for fragment-based drug discovery.<\/span><\/a><span> Trends in Pharmacological Sciences.\u00a0<\/span><\/li>\n<li><span>Kozakov D, Hall DR, Napoleon RL, Yueh C, Whitty A, Vajda S. (2015). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/acs.jmedchem.5b00586\"><span>New frontiers in druggability.<\/span><\/a><span> Journal of Medicinal Chemistry.<\/span><\/li>\n<li><span>Xia B, Mamonov A, Leysen S, Allen KN, Strelkov SV et al.. (2015). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/jcc.23952\"><span>Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro.<\/span><\/a><span> Journal of Computational Chemistry.\u00a0<\/span><\/li>\n<li><span>Mirzaei H, Zarbafian S, Villar E, Mottarella S, Beglov D et al.. (2015). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/ct500155t\"><span>Energy Minimization on Manifolds for Docking Flexible Molecules.<\/span><\/a><span> Journal of Chemical Theory and Computation.<\/span><\/li>\n<li><span>Moghadasi M, Mirzaei H, Mamonov A, Vakili P, Vajda S et al.. (2015). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/ci500380a\"><span>The Impact of Side-Chain Packing on Protein Docking Refinement.<\/span><\/a><span> Journal of Chemical Information and Modeling.<\/span><\/li>\n<li><span>Kozakov D, Hall DR, Jehle S, Luo L, Ochiana SO et al.. (2015). <\/span><a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.1501567112\"><span>Ligand deconstruction: Why some fragment binding positions are conserved and others are not.<\/span><\/a><span> Proceedings of the National Academy of Sciences.<\/span><\/li>\n<\/ul>\n<h2><b>2014<\/b><\/h2>\n<ul>\n<li><span>Villar EA, Beglov D, Chennamadhavuni S, Porco JA, Kozakov D et al.. (2014).\u00a0 <\/span><a href=\"http:\/\/www.nature.com\/nchembio\/journal\/v10\/n9\/full\/nchembio.1584.html\"><span>How proteins bind macrocycles.<\/span><\/a><span> Nature Chemical Biology.\u00a0<\/span><\/li>\n<li><span>Shin U, Williams DE, Kozakov D, Hall DR, Beglov D et al.. (2014). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.ab.2013.10.026\"><span>Stimulators of translation identified during a small molecule screening campaign.<\/span><\/a><span> Analytical Biochemistry.\u00a0<\/span><\/li>\n<li><span>Bohnuud T, Kozakov D, Vajda S. (2014). <\/span><a href=\"http:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1003872\"><span>Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces.<\/span><\/a><span> PLoS Computational Biology<\/span><\/li>\n<li><span>Chowdhury R, Beglov D, Moghadasi M, Paschalidis IC, Vakili P et al.. (2014). <\/span><a href=\"http:\/\/pubs.acs.org\/doi\/10.1021\/ct400474w\"><span>Efficient maintenance and update of nonbonded lists in macromolecular simulations.<\/span><\/a><span> Journal of Chemical Theory and Computation.<\/span><\/li>\n<li><span>Mottarella SE, Beglov D, Beglova N, Nugent MA, Kozakov D, Vajda S. (2014). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/ci500115j\"><span>Docking server for the identification of heparin binding sites on proteins.<\/span><\/a><span> Journal of Chemical Information and Modeling.<\/span><\/li>\n<li><span>Bogorad AM, Xia B, Sandor DG, Mamonov AB, Cafarella TR et al.. (2014). <\/span><a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/bi500346u\"><span>Insights into the architecture of the eIF2B\u03b1\/\u03b2\/\u03b3 regulatory subcomplex.<\/span><\/a><span> Biochemistry.<\/span><\/li>\n<li><span>Kozakov D, Li K, Hall DR, Beglov D, Zheng J et al.. (2014). <\/span><a href=\"https:\/\/elifesciences.org\/content\/3\/e01370\"><span>Encounter complexes and dimensionality reduction in protein protein association.<\/span><\/a><span> eLife.<\/span><\/li>\n<li><span>Vakili P, Mirzaei H, Zarbafian S, Paschalidis IC, Kozakov D, Vajda S. (2014). <\/span><a href=\"https:\/\/doi.org\/10.1109\/CDC.2014.7040301\"><span>Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach.<\/span><\/a><span> 53rd IEEE Conference on Decision and Control.<\/span><\/li>\n<\/ul>\n<h2><b>2013<\/b><\/h2>\n<ul>\n<li><span>Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA et al.. (2013). <\/span><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.24356\/abstract\"><span>Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics.<\/span><\/li>\n<li><span>Lavi A, Ngan CH, Movshovitz-Attias D, Bohnuud T, Yueh C et al.. (2013). <\/span><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.24422\/abstract\"><span>Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics.\u00a0<\/span><\/li>\n<li><span>Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B et al.. (2013). <\/span><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.24403\/abstract\"><span>How good is automated protein docking?<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics.<\/span><\/li>\n<li><span>Vajda S, Hall DR, Kozakov D. (2013). <\/span><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.24343\/abstract\"><span>Sampling and scoring: A marriage made in heaven.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics.<\/span><\/li>\n<li><span>Grove LE, Hall DR, Beglov D, Vajda S, Kozakov D. (2013). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btt102\"><span>FTFlex: Accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. <\/span><\/a><span>Bioinformatics.<\/span><\/li>\n<li><span>Golden MS, Cote SM, Sayeg M, Zerbe BS, Villar EA et al.. (2013). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/ja400914z\"><span>Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-\u03baB Essential Modulator (NEMO)\/IKK\u03b2 Protein-Protein Interface.<\/span><\/a><span> Journal of the American Chemical Society, 130318121200001.<\/span><\/li>\n<\/ul>\n<h2><b>2012<\/b><\/h2>\n<ul>\n<li><span>Zerbe BS, Hall DR, Vajda S, Whitty A, Kozakov D. (2012). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/ci300175u\"><span>Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces.<\/span><\/a><span> Journal of chemical information and modeling.\u00a0<\/span><\/li>\n<li><span>Ngan CH, Hall DR, Zerbe BS, Grove LE, Kozakov D, Vajda S. (2012). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr651\"><span>FTSite: high accuracy detection of ligand binding sites on unbound protein structures.<\/span><\/a><span> Bioinformatics, 28(2), 286\u2013287.<\/span><\/li>\n<li><span>Ngan CH, Bohnuud T, Mottarella SE, Beglov D, Villar EA et al.. (2012). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/nar\/gks441\"><span>FTMAP: extended protein mapping with user-selected probe molecules.<\/span><\/a><span> Nucleic Acids Research, 40(W1), W271 \u2013 W275.\u00a0<\/span><\/li>\n<li><span>Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D. (2012). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/ct300272j\"><span>Rigid Body Energy Minimization on Manifolds for Molecular Docking.<\/span><\/a><span> Journal of Chemical Theory and Computation, 120821123549006.\u00a0<\/span><\/li>\n<li><span>Hingtgen S, Kasmieh R, Elbayly E, Nesterenko I, Figueiredo J-L et al.. (2012). <\/span><a href=\"http:\/\/dx.doi.org\/10.1371\/journal.pone.0040234.g006\"><span>A First-Generation Multi-Functional Cytokine for Simultaneous Optical Tracking and Tumor Therapy.<\/span><\/a><span> PLoS ONE, 7(7), e40234.\u00a0<\/span><\/li>\n<li><span>Hall DR, Ngan CH, Zerbe BS, Kozakov D, Vajda S. (2012b). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/ci200468p\"><span>Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery.<\/span><\/a><span> Journal of Chemical Information and Modeling, 52(1), 199\u2013209.<\/span><\/li>\n<li><span>Hall DR, Kozakov D, Vajda S. (2012a). <\/span><a href=\"https:\/\/link.springer.com\/protocol\/10.1007%2F978-1-61779-465-0_2\"><span>Analysis of Protein Binding Sites by Computational Solvent Mapping.<\/span><\/a><span> Methods in Molecular Biology (Vol. 819). New York, NY: Springer New York.<\/span><\/li>\n<li><span>Brenke R, Hall DR, Chuang G-Y, Comeau SR, Bohnuud T et al.. (2012). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/bts493\"><span>Application of asymmetric statistical potentials to antibody-protein docking.<\/span><\/a><span> Bioinformatics, 28(20), 2608\u20132614.\u00a0<\/span><\/li>\n<li><span>Bohnuud T, Beglov D, Ngan CH, Zerbe BS, Hall DR et al.. (2012). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/nar\/gks519\"><span>Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde.<\/span><\/a><span> Nucleic Acids Research, 40(16), 7644\u20137652.\u00a0<\/span><\/li>\n<li><span>Beglov D, Hall DR, Brenke R, Shapovalov MV, Dunbrack RL et al.. (2012). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.23222\"><span>Minimal ensembles of side chain conformers for modeling protein-protein interactions. <\/span><\/a><span>Proteins: Structure, Function, and Bioinformatics, 80(2), 591\u2013601.\u00a0<\/span><\/li>\n<\/ul>\n<h2><b>2011<\/b><\/h2>\n<ul>\n<li><span>Kozakov D, Hall DR, Chuang G-Y, Cencic R, Brenke R et al.. (2011). <\/span><a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.1101835108\"><span>Structural conservation of druggable hot spots in protein-protein interfaces.<\/span><\/a><span> Proceedings of the National Academy of Sciences, 108(33), 13528\u201313533.\u00a0<\/span><\/li>\n<li><span>Hall DR, Grove LE, Yueh C, Ngan CH, Kozakov D, Vajda S. (2011). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/ja207914y\"><span>Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme.<\/span><\/a><span> Journal of the American Chemical Society, 133(51), 20668\u201320671.<\/span><\/li>\n<li><span>Cencic R, Hall DR, Robert F, Du Y, Min J et al.. (2011b). <\/span><a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.1011477108\"><span>Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F.<\/span><\/a><span> Proceedings of the National Academy of Sciences of the United States of America, 108(3).\u00a0<\/span><\/li>\n<li><span>Cencic R, Desforges M, Hall DR, Kozakov D, Du Y et al.. (2011a). <\/span><a href=\"http:\/\/dx.doi.org\/10.1128\/JVI.00078-11\"><span>Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication.<\/span><\/a><span> Journal of Virology, 85(13), 6381\u20136389.<\/span><\/li>\n<li><span>Buhrman G, O\u2032Connor C, Zerbe BS, Kearney BM, Napoleon R et al.. (2011). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2011.09.011\"><span>Analysis of Binding Site Hot Spots on the Surface of Ras GTPase.<\/span><\/a><span> Journal of Molecular Biology, 413(4), 773\u2013789.<\/span><\/li>\n<\/ul>\n<h2><b>2010<\/b><\/h2>\n<ul>\n<li><span>Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR et al.. (2010b). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.22835\"><span>Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics, 78(15), 3124\u20133130.<\/span><\/li>\n<li><span>Kozakov D, Chuang G-Y, Beglov D, Vajda S. (2010a). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.tibs.2010.03.006\"><span>Where does amantadine bind to the influenza virus M2 proton channel? <\/span><\/a><span>Trends in Biochemical Sciences.\u00a0<\/span><\/li>\n<li><span>Chuang G-Y, Mehra-Chaudhary R, Ngan CH, Zerbe BS, Kozakov D et al.. (2010). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/pro.446\"><span>Domain motion and inter-domain hot spots in a multi-domain enzyme.<\/span><\/a><span> Protein Science.\u00a0<\/span><\/li>\n<\/ul>\n<h2><b>2009<\/b><\/h2>\n<ul>\n<li><span>Vajda S, Kozakov D. (2009). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.sbi.2009.02.008\"><span>Convergence and combination of methods in protein\u2013protein docking.<\/span><\/a><span> Current Opinion in Structural Biology, 19(2), 164\u2013170.\u00a0<\/span><\/li>\n<li><span>Schwede T, Sali A, Honig B, Levitt M, Berman HM et al.. (2009). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.str.2008.12.014\"><span>Outcome of a Workshop on Applications of Protein Models in Biomedical Research.<\/span><\/a><span> Structure, 17(2), 151\u2013159.\u00a0<\/span><\/li>\n<li><span>Ngan CH, Beglov D, Rudnitskaya AN, Kozakov D, Waxman DJ, Vajda S. (2009). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/bi901578n\"><span>The Structural Basis of Pregnane X Receptor Binding Promiscuity.<\/span><\/a><span> Biochemistry, 48(48), 11572\u201311581.\u00a0<\/span><\/li>\n<li><span>Landon MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JMM et al.. (2009). <\/span><a href=\"http:\/\/dx.doi.org\/10.1007\/s10822-009-9283-2\"><span>Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase.<\/span><\/a><span> Journal of Computer-Aided Molecular Design, 23(8), 491\u2013500.<\/span><\/li>\n<li><span>Beglov D, Brenke R, Chuang G-Y, Hall DR, Landon MR et al.. (2009). <\/span><a href=\"https:\/\/www.taylorfrancis.com\/books\/9780429139437\/chapters\/10.1201\/9781420070071-17\"><span>Identification of Druggable Hot Spots on Proteins and in Protein Protein Interfaces.<\/span><\/a><span> In Computational Protein-Protein Interactions.<\/span><\/li>\n<li><span>Chuang G-Y, Kozakov D, Brenke R, Beglov D, Guarnieri F, Vajda S. (2009). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.bpj.2009.09.004\"><span>Binding Hot Spots and Amantadine Orientation in the Influenza A Virus M2 Proton Channel.<\/span><\/a><span> Biophysical Journal, 97(10), 2846\u20132853.\u00a0<\/span><\/li>\n<li><span>Brenke R, Kozakov D, Chuang G-Y, Beglov D, Hall DR et al.. (2009). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btp036\"><span>Fragment-based identification of druggable \u201chot spots\u201d of proteins using Fourier domain correlation techniques.<\/span><\/a><span> Bioinformatics, 25(5), 621\u2013627.<\/span><\/li>\n<li><span>Beglov D, Lee C-J, De Biasio A, Kozakov D, Brenke R et al.. (2009). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.22519\"><span>Structural insights into recognition of \u03b22-glycoprotein I by the lipoprotein receptors.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics, 77(4), 940\u2013949.<\/span><\/li>\n<\/ul>\n<h2><b>2008<\/b><\/h2>\n<ul>\n<li><span>Ritchie DW, Kozakov D, Vajda S. (2008). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btn334\"><span>Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.<\/span><\/a><span> Bioinformatics, 24(17), 1865\u20131873.\u00a0<\/span><\/li>\n<li><span>Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D et al.. (2008). <\/span><a href=\"http:\/\/dx.doi.org\/10.1111\/j.1747-0285.2007.00614.x\"><span>Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble.<\/span><\/a><span> Chemical Biology &amp; Drug Design, 71(2), 106\u2013116.<\/span><\/li>\n<li><span>Kozakov D, Schueler\u2010Furman O, Vajda S. (2008). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.21997\"><span>Discrimination of near\u2010native structures in protein\u2013protein docking by testing the stability of local minima.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics, 72(3), 993\u20131004.<\/span><\/li>\n<li><span>Shen Y, Paschalidis IC, Vakili P, Vajda S. (2008). <\/span><a href=\"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.1000191\"><span>Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes.<\/span><\/a><span> PLoS Computational Biology, 4(10), e1000191.<\/span><\/li>\n<li><span>Chuang G-Y, Kozakov D, Brenke R, Comeau SR, Vajda S. (2008). <\/span><a href=\"http:\/\/dx.doi.org\/10.1529\/biophysj.108.135814\"><span>DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking.<\/span><\/a><span> Biophysical Journal, 95(9), 4217\u20134227.\u00a0<\/span><\/li>\n<\/ul>\n<h2><b>2007<\/b><\/h2>\n<ul>\n<li><span>Silberstein M, Damborsky J, Vajda S. (2007). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/bi700336y\"><span>Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10.<\/span><\/a><span> Biochemistry, 46(32), 9239\u20139249.<\/span><\/li>\n<li><span>Shen Y, Brenke R, Kozakov D, Comeau SR, Beglov D, Vajda S. (2007). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.21754\"><span>Docking with PIPER and refinement with SDU in rounds 6\u201311 of CAPRI.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics, 69(4), 734\u2013742.<\/span><\/li>\n<li><span>Prasad JC, Goldstone JV, Camacho CJ, Vajda S, Stegeman JJ. (2007). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/bi062320m\"><span>Ensemble Modeling of Substrate Binding to Cytochromes P450:\u00a0 Analysis of Catalytic Differences between CYP1A Orthologs.<\/span><\/a><span> Biochemistry, 46(10), 2640\u20132654.<\/span><\/li>\n<li><span>Paschalidis IC, Shen Y, Vakili P, Vajda S. (2007). <\/span><a href=\"http:\/\/dx.doi.org\/10.1109\/TAC.2007.894518\"><span>SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking.<\/span><\/a><span> IEEE Transactions on Automatic Control, 52(4), 664\u2013676.\u00a0<\/span><\/li>\n<li><span>Landon MR, Lancia, Jr. DR, Yu J, Thiel SC, Vajda S. (2007).<\/span> <a href=\"http:\/\/dx.doi.org\/10.1021\/jm061134b\"><span>Identification of Hot Spots within Druggable Binding Regions by Computational Solvent Mapping of Proteins.<\/span><\/a><span> Journal of Medicinal Chemistry, 50(6), 1231\u20131240.\u00a0<\/span><\/li>\n<li><span>Comeau SR, Kozakov D, Brenke R, Shen Y, Beglov D, Vajda S.. (2007). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.21795\"><span>ClusPro: Performance in CAPRI rounds 6\u201311 and the new server.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics, 69(4), 781\u2013785.<\/span><\/li>\n<li><span>Aslan FM, Yu Y, Vajda S, Mohr SC, Cantor CR. (2007). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.jbiotec.2006.08.014\"><span>Engineering a novel, stable dimeric streptavidin with lower isoelectric point.<\/span><\/a><span> Journal of Biotechnology, 128(2), 213\u2013225.\u00a0<\/span><\/li>\n<\/ul>\n<h2><b>2006<\/b><\/h2>\n<ul>\n<li><span>Vajda S, Guarnieri F. (2006). <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16729732\"><span>Characterization of protein-ligand interaction sites using experimental and computational methods.<\/span><\/a><span> Current Opinion in Drug Discovery and Development, 9(3), 363\u2013369.<\/span><\/li>\n<li><span>Vajda S. (2006b). <\/span><a href=\"https:\/\/www.fasebj.org\/doi\/abs\/10.1096\/fasebj.20.5.A851-b\"><span>Classification of protein complexes based on the biophysics of association.<\/span><\/a><span> ASBMB Annual Meeting.<\/span><\/li>\n<li><span>Vajda S. (2006a). Computational Mapping of Proteins for Fragment Based Drug Design. Keystone Symposium on Structure Based Drug Discovery.<\/span><\/li>\n<li><span>Silberstein M, Landon MR, Wang YE, Perl A, Vajda S. (2006). <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/17503352\"><span>Computational methods for functional site identification suggest a substrate access channel in transaldolase.<\/span><\/a><span> Genome Informatics, 17(1), 13\u201322.<\/span><\/li>\n<li><span>Paschalidis IC, Shen Y, Vakili P, Vajda S. (2006). Protein Docking by Exploiting Multi-dimensional Energy Funnels. IEEE 2006 International Conference of EMBS.<\/span><\/li>\n<li><span>Paschalidis IC, Shen Y, Vakili P, Vajda S. (2006). <\/span><a href=\"http:\/\/dx.doi.org\/10.1109\/IEMBS.2006.260790\"><span>Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.<\/span><\/a><span> Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 5330\u20135333.\u00a0<\/span><\/li>\n<li><span>Landon MR, Yu J, Thiel SC, Lancia, Jr. DR, Vajda S. (2006). <\/span><a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/jm061134b\"><span>Identification of \u201cHot Spots\u201d in Druggable Binding Pockets by Computational Solvent Mapping of Proteins.<\/span><\/a><span> Journal of Medicinal Chemistry<\/span><\/li>\n<li><span>Landon MR, Lancia, Jr. DR, Clodfelter KH, Vajda S. (2006). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmgm.2005.08.004\"><span>Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns.<\/span><\/a><span> Journal of Molecular Graphics and Modelling, 24(6), 426\u2013433.\u00a0<\/span><\/li>\n<li><span>Kozakov D, Brenke R, Comeau SR, Vajda S. (2006). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.21117\"><span>PIPER: An FFT-based protein docking program with pairwise potentials.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics, 65(2), 392\u2013406.<\/span><\/li>\n<li><span>Kaya T, Mohr SC, Waxman DJ, Vajda S. (2006). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/tx050301s\"><span>Computational Screening of Phthalate Monoesters for Binding to PPAR\u03b3.<\/span><\/a><span> Chemical Research in Toxicology, 19(8), 999\u20131009.\u00a0<\/span><\/li>\n<li><span>Clodfelter KH, Waxman DJ, Vajda S. (2006). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/bi060343v\"><span>Computational Solvent Mapping Reveals the Importance of Local Conformational Changes for Broad Substrate Specificity in Mammalian Cytochromes P450.<\/span><\/a><span> Biochemistry, 45(31), 9393\u20139407.\u00a0<\/span><\/li>\n<\/ul>\n<h2><b>2005<\/b><\/h2>\n<ul>\n<li><span>Vajda S. (2005). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.20554\"><span>Classification of protein complexes based on docking difficulty.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics, 60(2), 176\u2013180.\u00a0<\/span><\/li>\n<li><span>Sheu S-H, Kaya T, Waxman DJ, Vajda S. (2005). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/bi048032c\"><span>Exploring the Binding Site Structure of the PPAR\u03b3 Ligand-Binding Domain by Computational Solvent Mapping.<\/span><\/a><span> Biochemistry, 44(4), 1193\u20131209.\u00a0<\/span><\/li>\n<li><span>Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. (2005). <\/span><a href=\"http:\/\/dx.doi.org\/10.1529\/biophysj.104.058768\"><span>Optimal Clustering for Detecting Near-Native Conformations in Protein Docking.<\/span><\/a><span> Biophysical Journal, 89(2), 867\u2013875.\u00a0<\/span><\/li>\n<li><span>Comeau SR, Vajda S, Camacho CJ. (2005).<\/span> <a href=\"http:\/\/dx.doi.org\/10.1002\/prot.20564\"><span>Performance of the first protein docking server ClusPro in CAPRI rounds 3-5.<\/span><\/a><span> Proteins: Structure, Function, and Bioinformatics, 60(2), 239\u2013244.\u00a0<\/span><\/li>\n<li><span>Comeau SR, Camacho CJ. (2005). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.jsb.2005.03.006\"><span>Predicting oligomeric assemblies: N-mers a primer.<\/span><\/a><span> Journal of Structural Biology, 150(3), 233\u2013244.<\/span><\/li>\n<\/ul>\n<h2><b>2004<\/b><\/h2>\n<ul>\n<li><span>Vajda S, Camacho CJ. (2004). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.tibtech.2004.01.006\"><span>Protein\u2013protein docking: is the glass half-full or half-empty? <\/span><\/a><span>Trends in Biotechnology, 22(3), 110\u2013116.\u00a0<\/span><\/li>\n<li><span>Sheu S-H, Lancia, Jr. DR, Clodfelter KH, Landon MR, Vajda S. (2004). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/nar\/gki091\"><span>PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.<\/span><\/a><span> Nucleic Acids Research, 33(Database), D206 \u2013 D211.\u00a0<\/span><\/li>\n<li><span>Rajamani D, Thiel SC, Vajda S, Camacho CJ. (2004). <\/span><a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0401942101\"><span>Anchor residues in protein-protein interactions.<\/span><\/a><span> Proceedings of the National Academy of Sciences, 101(31), 11287\u201311292.\u00a0<\/span><\/li>\n<li><span>Prasad JC, Vajda S, Camacho CJ. (2004). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/nar\/gkh456\"><span>Consensus alignment server for reliable comparative modeling with distant templates. <\/span><\/a><span>Nucleic Acids Research, 32(Web Server), W50 \u2013 W54.\u00a0<\/span><\/li>\n<li><span>Comeau SR, Gatchell DW, Vajda S, Camacho CJ (2004b). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/nar\/gkh354\"><span>ClusPro: a fully automated algorithm for protein-protein docking.<\/span><\/a><span> Nucleic Acids Research, 32(Web Server), W96 \u2013 W99.<\/span><\/li>\n<li><span>Comeau SR, Gatchell DW, Vajda S, Camacho CJ. (2004a). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btg371\"><span>ClusPro: an automated docking and discrimination method for the prediction of protein complexes.<\/span><\/a><span> Bioinformatics, 20(1), 45\u201350.\u00a0<\/span><\/li>\n<\/ul>\n<h2><b>2003<\/b><\/h2>\n<ul>\n<li><span>Silberstein M, Dennis S, Brown L, Kortvelyesi T, Clodfelter KH, Vajda S. (2003). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2003.08.019\"><span>Identification of Substrate Binding Sites in Enzymes by Computational Solvent Mapping.<\/span><\/a><span> Journal of Molecular Biology, 332(5), 1095\u20131113.\u00a0<\/span><\/li>\n<li><span>Prasad JC, Comeau SR, Vajda S, Camacho CJ. (2003). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btg211\"><span>Consensus alignment for reliable framework prediction in homology modeling.<\/span><\/a><span> Bioinformatics, 19(13), 1682\u20131691.<\/span><\/li>\n<li><span>Murphy J, Gatchell DW, Prasad JC, Vajda S. (2003). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.10473\"><span>Combination of scoring functions improves discrimination in protein-protein docking.<\/span><\/a><span> Proteins: Structure, Function, and Genetics, 53(4), 840\u2013854.\u00a0<\/span><\/li>\n<li><span>Kortvelyesi T, Silberstein M, Dennis S, Vajda S. (2003). <\/span><a href=\"http:\/\/dx.doi.org\/10.1023\/A:1025369923311\"><span>Improved mapping of protein binding sites.<\/span><\/a><span> Journal of Computer-Aided Molecular Design, 17(2\/4), 173\u2013186.<\/span><\/li>\n<li><span>Kortvelyesi T, Dennis S, Silberstein M, Brown L, Vajda S. (2003). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.10287\"><span>Algorithms for computational solvent mapping of proteins.<\/span><\/a><span> Proteins: Structure, Function, and Genetics, 51(3), 340\u2013351.\u00a0<\/span><\/li>\n<li><span>Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJE et al.. (2003). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.10381\"><span>CAPRI: A Critical Assessment of PRedicted Interactions.<\/span><\/a><span> Proteins: Structure, Function, and Genetics, 52(1), 2\u20139.<\/span><\/li>\n<li><span>Camacho CJ, Gatchell DW. (2003). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.10394\"><span>Successful discrimination of protein interactions. <\/span><\/a><span>Proteins: Structure, Function, and Genetics, 52(1), 92\u201397.\u00a0<\/span><\/li>\n<\/ul>\n<h2><b>2002<\/b><\/h2>\n<ul>\n<li><span>Valk\u00f3 PP, Vajda S.. (2002). <\/span><a href=\"http:\/\/dx.doi.org\/10.1080\/10682760290004294\"><span>Inversion of Noise-Free Laplace Transforms: Towards a Standardized Set of Test Problems. <\/span><\/a><span>Inverse Problems in Engineering, 10(5), 467\u2013483.\u00a0<\/span><\/li>\n<li><span>Vajda S, Vakser IA, Sternberg MJE, Janin J. (2002). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/prot.10112\"><span>Modeling of protein interactions in genomes.<\/span><\/a><span> Proteins: Structure, Function, and Genetics, 47(4), 444\u2013446.\u00a0<\/span><\/li>\n<li><span>Dennis S, Vajda S. (2002). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/jcc.10026\"><span>Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins.<\/span><\/a><span> Journal of Computational Chemistry, 23(3), 319\u2013334.\u00a0<\/span><\/li>\n<li><span>Dennis S, Kortvelyesi T, Vajda S. (2002). <\/span><a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.062398499\"><span>Computational mapping identifies the binding sites of organic solvents on proteins.<\/span><\/a><span> Proceedings of the National Academy of Sciences, 99(7), 4290\u20134295.<\/span><\/li>\n<li><span>Camacho CJ, Vajda S. (2002). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/S0959-440X(02)00286-5\"><span>Protein\u2013protein association kinetics and protein docking.<\/span><\/a><span> Current Opinion in Structural Biology, 12(1), 36\u201340.<\/span><\/li>\n<\/ul>\n<h2><b>2001<\/b><\/h2>\n<ul>\n<li><span>Kimura SR, Brower RC, Vajda S, Camacho CJ. (2001). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/S0006-3495(01)76044-4\"><span>Dynamical View of the Positions of Key Side Chains in Protein-Protein Recognition.<\/span><\/a><span> Biophysical Journal, 80(2), 635\u2013642.\u00a0<\/span><\/li>\n<li><span>Camacho CJ, Vajda S. (2001b). <\/span><a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.181147798\"><span>Protein docking along smooth association pathways.<\/span><\/a><span> Proceedings of the National Academy of Sciences, 98(19), 10636\u201310641.\u00a0<\/span><\/li>\n<li><span>Camacho CJ, Vajda S. (2001a). <\/span><a href=\"https:\/\/www.wiley.com\/en-us\/Drug+Receptor+Thermodynamics%3A+Introduction+and+Applications-p-9780471720423\"><span>Thermodynamic maps of receptor-ligand pairs reveal how some proteins bind.<\/span><\/a><span> Drug-Receptor Thermodynamics (pp. 581\u2013592). NY: Wiley.<\/span><\/li>\n<\/ul>\n<h2><b>2000-<\/b><\/h2>\n<ul>\n<li><span>Gatchell DW, Dennis S, Vajda S. (2000). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/1097-0134(20001201)41:4%3C518::AID-PROT90%3E3.0.CO;2-6\"><span>Discrimination of near-native protein structures from misfolded models by empirical free energy functions.<\/span><\/a><span> Proteins: Structure, Function, and Genetics, 41(4), 518\u2013534.\u00a0<\/span><\/li>\n<li><span>Dennis S, Camacho CJ, Vajda S. (2000b). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/(SICI)1097-0134(20000201)38:2%3C176::AID-PROT6%3E3.0.CO;2-O\"><span>Continuum electrostatic analysis of preferred solvation sites around proteins in solution.<\/span><\/a><span> Proteins: Structure, Function, and Genetics, 38(2), 176\u2013188.\u00a0<\/span><\/li>\n<li><span>Dennis S, Camacho CJ, Vajda S. (2000a). <\/span><a href=\"https:\/\/link.springer.com\/chapter\/10.1007\/978-1-4757-3218-4_14\"><span>Exploring potential solvation sites of proteins by multistart local minimization.<\/span><\/a><span> In Optimization in Computational Chemistry and Molecular Biology (pp. 243\u2013261). Kluwer Academic.<\/span><\/li>\n<li><span>Camacho CJ, Kimura SR, DeLisi C, Vajda S. (2000). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/S0006-3495(00)76668-9\"><span>Kinetics of Desolvation-Mediated Protein\u2013Protein Binding.<\/span><\/a><span> Biophysical Journal, 78(3), 1094\u20131105.<\/span><\/li>\n<li><span>Camacho CJ, Gatchell DW, Kimura SR, Vajda S. (2000). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/1097-0134(20000815)40:3%3C525::AID-PROT190%3E3.0.CO;2-F\"><span>Scoring docked conformations generated by rigid-body protein-protein docking.<\/span><\/a><span> Proteins: Structure, Function, and Genetics, 40(3), 525\u2013537.<\/span><\/li>\n<li><span>Esposito M, Venkatesh V, Otvos L, Weng Z, Vajda S et al.. (1999). <\/span><a href=\"https:\/\/www.jimmunol.org\/content\/163\/7\/4027\"><span>Human Transaldolase and Cross-Reactive Viral Epitopes Identified by Autoantibodies of Multiple Sclerosis Patients.<\/span><\/a><span> The Journal of Immunology, 163, 4027\u20134032.<\/span><\/li>\n<li><span>DeLisi C, Vajda S. (1999). <\/span><a href=\"http:\/\/dx.doi.org\/10.1109\/5992.764213\"><span>Computational problems in cell biology.<\/span><\/a><span> Computing in Science &amp; Engineering, 1(3), 26\u201332.\u00a0<\/span><\/li>\n<li><span>Camacho CJ, Weng Z, Vajda S, DeLisi C. (1999). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/S0006-3495(99)77281-4\"><span>Free Energy Landscapes of Encounter Complexes in Protein-Protein Association.<\/span><\/a><span> Biophysical Journal, 76(3), 1166\u20131178.\u00a0<\/span><\/li>\n<li><span>Zhang C, Brower RC, Kimura SR, Weng Z, Vajda S, DeLisi C. (1998). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/S0016-0032(97)00020-3\"><span>The waters of life.<\/span><\/a><span> Journal of the Franklin Institute, 335(2), 213\u2013240.\u00a0<\/span><\/li>\n<li><span>Vajda S. (1998). <\/span><a href=\"https:\/\/www.wiley.com\/en-us\/Encyclopedia+of+Computational+Chemistry%2C+5+Volume+Set-p-9780471965886\"><span>Conformational Analysis.<\/span><\/a><span> Encyclopedia of Computational Chemistry. Chichester: John Wiley &amp; Sons Ltd.<\/span><\/li>\n<li><span>Sano T, Vajda S, Cantor CR. (1998). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/S0378-4347(98)00316-8\"><span>Genetic engineering of streptavidin, a versatile affinity tag.<\/span><\/a><span> Journal of Chromatography B: Biomedical Sciences and Applications, 715(1), 85\u201391.\u00a0<\/span><\/li>\n<li><span>Reznik GO, Vajda S, Sano T, Cantor CR. (1998). <\/span><a href=\"https:\/\/www.pnas.org\/content\/95\/23\/13525\"><span>A streptavidin mutant with altered ligand-binding specificity.<\/span><\/a><span> Proceedings of the National Academy of Sciences, 95(23), 13525\u201313530.<\/span><\/li>\n<li><span>Janardhan A, Vajda S. (1998). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/pro.5560070812\"><span>Selecting near-native conformations in homology modeling: The role of molecular mechanics and solvation terms.<\/span><\/a><span> Protein Science, 7(8), 1772\u20131780.\u00a0<\/span><\/li>\n<li><span>Weng Z, DeLisi C, Vajda S. (1997). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/pro.5560060918\"><span>Empirical free energy calculation: Comparison to calorimetric data.<\/span><\/a><span> Protein Science, 6(9), 1976\u20131984.\u00a0<\/span><\/li>\n<li><span>Vajda S, Sippl M, Novotny J. (1997). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/S0959-440X(97)80029-2\"><span>Empirical potentials and functions for protein folding and binding.<\/span><\/a><span> Current Opinion in Structural Biology, 7(2), 222\u2013228.\u00a0<\/span><\/li>\n<li><span>Sano T, Vajda S, Smith CL, Cantor CR. (1997). <\/span><a href=\"https:\/\/www.pnas.org\/content\/94\/12\/6153\"><span>Engineering subunit association of multisubunit proteins: A dimeric streptavidin.<\/span><\/a><span> Proceedings of the National Academy of Sciences, 94(12), 6153\u20136158.<\/span><\/li>\n<li><span>Weng Z, Vajda S, DeLisi C. (1996). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/pro.5560050406\"><span>Prediction of protein complexes using empirical free energy functions.<\/span><\/a><span> Protein Science, 5, 614\u2013626.<\/span><\/li>\n<li><span>Sezerman U, Vajda S, DeLisi C. (1996). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/pro.5560050706\"><span>Free energy mapping of class I MHC molecules and structural determination of bound peptides.<\/span><\/a><span> Protein Science, 5(7), 1272\u20131281.\u00a0<\/span><\/li>\n<li><span>Sano T, Vajda S, Reznik GO, Smith CL, Cantor CR. (1996). <\/span><a href=\"http:\/\/dx.doi.org\/10.1111\/j.1749-6632.1996.tb33229.x\"><span>Molecular Engineering of Streptavidin.<\/span><\/a><span> Annals of the New York Academy of Sciences, 799(Enzyme Eng), 383\u2013390.<\/span><\/li>\n<li><span>Reznik GO, Vajda S, Smith CL, Cantor CR, Sano T. (1996). <\/span><a href=\"http:\/\/dx.doi.org\/10.1038\/nbt0896-1007\"><span>Streptavidins with intersubunit crosslinks have enhanced stability.<\/span><\/a><span> Nature Biotechnology, 14(8), 1007\u20131011.\u00a0<\/span><\/li>\n<li><span>Luidens MK, Figge J, Breese K, Vajda S. (1996). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/(SICI)1097-0282(199609)39:3%3C367::AID-BIP8%3E3.0.CO;2-M\"><span>Predicted and trifluoroethanol-induced \u03b1-helicity of polypeptides.<\/span><\/a><span> Biopolymers, 39(3), 367\u2013376.<\/span><\/li>\n<li><span>King B, Vajda S, DeLisi C. (1996). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/0014-5793(96)00276-1\"><span>Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors.<\/span><\/a><span> FEBS Letters, 384(1), 87\u201391.<\/span><\/li>\n<li><span>Gulukota K, Vajda S, DeLisi C. (1996). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/(SICI)1096-987X(199603)17:4%3C418::AID-JCC4%3E3.0.CO;2-X\"><span>Peptide docking using dynamic programming.<\/span><\/a><span> Journal of Computational Chemistry, 17(4), 418\u2013428.\u00a0<\/span><\/li>\n<li><span>Vajda S, Weng Z, DeLisi C. (1995). <\/span><a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/8.11.1081\"><span>Extracting hydrophobicity parameters from solute partition and protein mutation\/unfolding experiments.<\/span><\/a><span> &#8220;Protein Engineering, Design and Selection&#8221;, 8(11), 1081\u20131092.<\/span><\/li>\n<li><span>Rosenfeld R, Vajda S, DeLisi C. (1995). <\/span><a href=\"http:\/\/dx.doi.org\/10.1146\/annurev.bb.24.060195.003333\"><span>Flexible Docking and Design.<\/span><\/a><span> Annual Review of Biophysics and Biomolecular Structure, 24(1), 677\u2013700.\u00a0<\/span><\/li>\n<li><span>Rosenfeld R, Zheng Q, Vajda S, DeLisi C. (1995). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/1050-3862(95)00107-7\"><span>Flexible docking of peptides to class I major-histocompatibility-complex receptors.<\/span><\/a><span> Genetic Analysis: Biomolecular Engineering, 12(1), 1\u201321.\u00a0<\/span><\/li>\n<li><span>Vajda S, Weng Z, Rosenfeld R, DeLisi C. (1994). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/bi00251a004\"><span>Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies.<\/span><\/a><span> Biochemistry, 33(47), 13977\u201313988.\u00a0<\/span><\/li>\n<li><span>Vajda S, Rabitz H. (1994). <\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/j100071a016\"><span>Identifiability and Distinguishability of General Reaction Systems.<\/span><\/a><span> The Journal of Physical Chemistry, 98(20), 5265\u20135271.<\/span><\/li>\n<li><span>Godfrey KR, Chapman MJ, Vajda S. (1994). <\/span><a href=\"http:\/\/dx.doi.org\/10.1007\/BF02353330\"><span>Identifiability and indistinguishability of nonlinear pharmacokinetic models.<\/span><\/a><span> Journal of Pharmacokinetics and Biopharmaceutics, 22(3), 229\u2013251.\u00a0<\/span><\/li>\n<li><span>Buturovi\u0107 LJ, Smith TF, Vajda S. (1994). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/jcc.540150305\"><span>Finite-state and reduced-parameter representations of protein backbone conformations.<\/span><\/a><span> Journal of Computational Chemistry, 15(3), 300\u2013312.<\/span><\/li>\n<li><span>Zheng Q, Rosenfeld R, Vajda S, DeLisi C. (1993b). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/pro.5560020806\"><span>Determining protein loop conformation using scaling-relaxation techniques.<\/span><\/a><span> Protein Science, 2(8), 1242\u20131248.\u00a0<\/span><\/li>\n<li><span>Zheng Q, Rosenfeld R, Vajda S, DeLisi C. (1993a). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/jcc.540140508\"><span>Loop closure via bond scaling and relaxation.<\/span><\/a><span> Journal of Computational Chemistry, 14(5), 556\u2013565.<\/span><\/li>\n<li><span>Vajda S, Rabitz H. (1993). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/0009-2509(93)81066-5\"><span>Generalized parametric sensitivity: Application to a CSTR.<\/span><\/a><span> Chemical Engineering Science, 48(13), 2453\u20132461.<\/span><\/li>\n<li><span>Sezerman U, Vajda S, Cornette J, DeLisi C. (1993). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/pro.5560021105\"><span>Toward computational determination of peptide-receptor structure.<\/span><\/a><span> Protein Science, 2(11), 1827\u20131843.\u00a0<\/span><\/li>\n<li><span>Rosenfeld R, Zheng Q, Vajda S, DeLisi C. (1993). <\/span><a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.1993.1607\"><span>Computing the Structure of Bound Peptides.<\/span><\/a><span> Journal of Molecular Biology, 234(3), 515\u2013521.\u00a0<\/span><\/li>\n<li><span>Rao S, Zhu Q-L, Vajda S, Smith T. (1993). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/0014-5793(93)81555-E\"><span>The local information content of the protein structural database.<\/span><\/a><span> FEBS Letters, 322(2), 143\u2013146.<\/span><\/li>\n<li><span>Figge J, Breese K, Vajda S, Zhu Q-L, Eisele L et al.. (1993). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/pro.5560020204\"><span>The binding domain structure of retinoblastoma-binding proteins.<\/span><\/a><span> Protein Science, 2(2), 155\u2013164.<\/span><\/li>\n<li><span>Vajda S, Rabitz H. (1992). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/0009-2509(92)80232-2\"><span>Parametric sensitivity and self-similarity in thermal explosion theory.<\/span><\/a><span> Chemical Engineering Science, 47(5), 1063\u20131078.\u00a0<\/span><\/li>\n<li><span>Jafri MS, Vajda S, Pasik P, Gillo B. (1992). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/S0006-3495(92)81583-7\"><span>A membrane model for cytosolic calcium oscillations. A study using Xenopus oocytes.<\/span><\/a><span> Biophysical Journal, 63(1), 235\u2013246.\u00a0<\/span><\/li>\n<li><span>Eisenfeld J, Vajda S, Sugar I, DeLisi C. (1991). <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/1872378\"><span>Constrained optimization and protein structure determination.<\/span><\/a><span> The American journal of physiology, 261(2 Pt 1):C376-86.<\/span><\/li>\n<li><span>Vajda S, Kataoka R, DeLisi C, Margalit H, Berzofsky JA, Cornette JL. (1990). <\/span><a href=\"http:\/\/dx.doi.org\/10.1146\/annurev.bb.19.060190.000441\"><span>Molecular Structure and Vaccine Design.<\/span><\/a><span> Annual Review of Biophysics and Biophysical Chemistry, 19(1), 69\u201382.\u00a0<\/span><\/li>\n<li><span>Vajda S, DeLisi C. (1990). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/bip.360291408\"><span>Determining minimum energy conformations of polypeptides by dynamic programming.<\/span><\/a><span> Biopolymers, 29(14), 1755\u20131772.\u00a0<\/span><\/li>\n<li><span>Chappell MJ, Godfrey KR, Vajda S. (1990). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/0025-5564(90)90055-4\"><span>Global identifiability of the parameters of nonlinear systems with specified inputs: A comparison of methods.<\/span><\/a><span> Mathematical Biosciences, 102(1), 41\u201373.\u00a0<\/span><\/li>\n<li><span>Vajda S, Distefano JJ, Godfrey KR, Fagarasan J. (1989). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/0025-5564(89)90042-4\"><span>Parameter space boundaries for unidentifiable compartmental models.<\/span><\/a><span> Mathematical Biosciences, 97(1), 27\u201360.<\/span><\/li>\n<li><span>Vajda S, Godfrey KR, Rabitz H. (1989). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/0025-5564(89)90024-2\"><span>Similarity transformation approach to identifiability analysis of nonlinear compartmental models.<\/span><\/a><span> Mathematical Biosciences, 93(2), 217\u2013248.\u00a0<\/span><\/li>\n<li><span>Vajda S, Rabitz H. (1989). <\/span><a href=\"http:\/\/dx.doi.org\/10.1109\/9.21105\"><span>State isomorphism approach to global identifiability of nonlinear systems.<\/span><\/a><span> IEEE Transactions on Automatic Control, 34(2), 220\u2013223.\u00a0<\/span><\/li>\n<li><span>Vajda S, Rabitz H, Walter E, Lecourtier Y. (1989). <\/span><a href=\"http:\/\/dx.doi.org\/10.1080\/00986448908940662\"><span>QUALITATIVE AND QUANTITATIVE IDENTIFIABILITY ANALYSIS OF NONLINEAR CHEMICAL KINETIC MODELS.<\/span><\/a><span> Chemical Engineering Communications, 83(1), 191\u2013219.<\/span><\/li>\n<li><span>Tur\u00e1nyi T, B\u00e9rces T, Vajda S. (1989). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/kin.550210203\"><span>Reaction rate analysis of complex kinetic systems.<\/span><\/a><span> International Journal of Chemical Kinetics, 21(2), 83\u201399.\u00a0<\/span><\/li>\n<li><span>Vajda S, Godfrey KR, Valko P. (1988). <\/span><a href=\"http:\/\/dx.doi.org\/10.1007\/BF01061863\"><span>Numerical deconvolution using system identification methods.<\/span><\/a><span> Journal of Pharmacokinetics and Biopharmaceutics, 16(1), 85\u2013107.\u00a0<\/span><\/li>\n<li><span>Vajda S, Rabitz H. (1988). I<\/span><a href=\"http:\/\/dx.doi.org\/10.1021\/j100314a024\"><span>dentifiability and distinguishability of first-order reaction systems.<\/span><\/a><span> The Journal of Physical Chemistry, 92(3), 701\u2013707.<\/span><\/li>\n<li><span>Vajda S, Valko P, Tur\u00e1nyi T. (1985). <\/span><a href=\"http:\/\/dx.doi.org\/10.1002\/kin.550170107\"><span>Principal component analysis of kinetic models.<\/span><\/a><span> International Journal of Chemical Kinetics, 17(1), 55\u201381.\u00a0<\/span><\/li>\n<li><span>Vajda S. (1984). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/0025-5564(84)90014-2\"><span>Structural equivalence and exhaustive compartmental modeling.<\/span><\/a><span> Mathematical Biosciences, 69(1), 57\u201375.\u00a0<\/span><\/li>\n<li><span>Vajda S. (1984). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/0025-5564(84)90023-3\"><span>Analysis of unique structural identifiability via submodels.<\/span><\/a><span> Mathematical Biosciences, 71(2), 125\u2013146.\u00a0<\/span><\/li>\n<li><span>Vajda S. (1982).<\/span> <a href=\"http:\/\/dx.doi.org\/10.1109\/TAC.1982.1103062\"><span>Further comments on &#8220;On parameter and structural identifiability: Nonunique observability\/reconstructibility for identifiable systems, other ambiguities, and new definitions&#8221;.<\/span><\/a><span> IEEE Transactions on Automatic Control, 27(5), 1136\u20131137.\u00a0<\/span><\/li>\n<li><span>Vajda S. (1981). <\/span><a href=\"http:\/\/dx.doi.org\/10.1016\/0025-5564(81)90012-2\"><span>Structural equivalence of linear systems and compartmental models.<\/span><\/a><span> Mathematical Biosciences, 55(1-2), 39\u201364. <\/span><\/li>\n<li><span>Vajda S. (1979). <\/span><a href=\"http:\/\/dx.doi.org\/10.1109\/TAC.1979.1102029\"><span>Comments on &#8220;Structural identifiability in linear time-invariant systems.<\/span><\/a><span> IEEE Transactions on Automatic Control, 24(3), 495\u2013496.<\/span><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>2020 Desta IT, Porter KA, Xia B, Kozakov D, Vajda S. (2020). Performance and Its Limits in Rigid Body Protein-Protein Docking. Structure. Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, et al.. (2020). ClusPro in rounds 38 to 45 of CAPRI: Toward combining template\u2010based methods with free docking. Proteins: Structure, Function, and Bioinformatics. 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