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  • Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzov M, et al. (2023) Mapping of Antibody Epitopes based on Docking and Homology Modeling. Proteins: Structure, Function, and Bioinformatics

  • Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, et al. (2023) High Accuracy Prediction of PROTAC Complex Structures. Journal of the American Chemical Society.

  • Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzon M, et al. (2023) The ClusPro AbEMap web server for the prediction of antibody epitopes. Nature Protocols

  • Egbert M, Jones G, Collins MR, Kozakov D, Vajda S. (2022) FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures. Journal of Molecular Biology

  • Jones G, Jindal A, Ghani U, Kotelnikov S, Egbert M, Hashemi N, et al. (2022) Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap. Acta Crystallographica Section D: Structural Biology

  • Jones G, Wakefield AE, Triplett K, Idrissa K, et al.. (2022) API Development Increases Access to Shared Computing Resources at Boston University. Journal of Software Engineering and Applications

  • Wakefield AE, Kozakov D, Vajda S. (2022) Mapping the binding sites of challenging drug targets. Current Opinion in Structural Biology

  • Ma S, Sun Z, Jing Y, McGann M, Vajda S, Enydey IJ. (2022) Use of Solvent Mapping for Characterizing the Binding Site and for Predicting the Inhibition of the Human Ether-a-Go-Go-Related K+ Channel. Chemical Research in Toxicology

  • Wakefield AE, Bajusz D, Kozakov D, Keseru GM, Vajda S. (2022) Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. Journal of Chemical Information and Modeling

  • Bajusz D, Wade WS, Satala G, Bojarski AJ, Ilaš J, et al.. (2021). Exploring protein hotspots by optimized fragment pharmacophores. Nature Communications.

  • Vajda S, Porter KA, Kozakov D. (2021). Progress toward improved understanding of antibody maturation. Current Opinion in Structural Biology.

  • Egbert M, Porter KA, Ghani U, Kotelnikov S, Nguyen T, et al.. (2021). Conservation ofbinding properties in protein models. Computational and Structural Biotechnology Journal.

  • Sotudian S, Desta IT, Hashemi N, Zarbafian S, Kozakov D, et al.. (2021). Improved cluster ranking in protein-protein docking using a regression approach. Computational and Structural Biotechnology Journal.

  • Egbert M, Ghani U, Ashizawa R, Kotelinikov S, Nhuyen T, et al.. (2021) Assessing the binding properties of CASP14 targets and models. Proteins: Structure, Function, and Bioinformatics

  • Wakefield AE, Yueh C, Beglov D, Castilho MS, Kozakov D, et al.. (2020). Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. Journal of Chemical Information and Modeling.

  • Desta IT, Porter KA, Xia B, Kozakov D, Vajda S. (2020). Performance and Its Limits in Rigid Body Protein-Protein Docking. Structure.

  • Alekseenko A, Kotelnikov S, Ignatov M, Egbert M, Kholodov Y, et al.. (2020). ClusPro LigTBM: Automated Template-Based Small Molecule Docking. Journal of Molecular Biology. 

  • Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, et al.. (2020). ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking. Structure, Function, and

  • Sun Z, Wakefield AE, Kolossvary I, Beglov D, Vajda S. (2020). Structure-Based Analysis of Cryptic-Site Opening. Structure.

  • Khramushin A, Marcu O, Alam N, Shimony O, Padhorny D, et al.. (2020) Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45. Proteins: Structure, Function, and Bioinformatics.

  • Zhong M, Lynch A, Muellers SN, Jehle S, Lingqi L et al.. (2020). Interaction Energetics and Druggability of the Protein–Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2). Biochemistry.

  • Porter KA, Padhorny D, Desta I, Ignatov M, Beglov D et al.. (2019). Template‐Based Modeling by ClusPro in CASP13 and the Potential for Using Co‐evolutionary Information in Docking. Proteins: Structure, Function, and Bioinformatics.

  • Vajda S, Emili A. (2019). Mapping global protein contacts. Science.

  • Egbert M, Whitty A, Keserű GM, Vajda S. (2019). Why some targets benefit from beyond rule of five drugs. Journal of Medicinal Chemistry.

  • Yueh C, Rettenmaier J, Xia B, Hall DR, Alekseenko A et al.. (2019). Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases. Journal of Medicinal Chemistry.

  • Wakefield AE, Mason JS, Vajda S, Keserű GM. (2019). Analysis of tractable allosteric sites in G protein-coupled receptors. Nature: Scientific Reports.

  • Froes TQ, Baldini RL, Vajda S, Castilho MS (2019). Structure-based druggability assessment of anti-virulence targets from Pseudomonas aeruginosa. Current Protein & Peptide Science.

  • Porter KA, Desta I, Kozakov D, Vajda S. (2019). What method to use for protein-protein docking? Current Opinion in Structural Biology.

  • Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A et al.. (2019). Allostery in Its Many Disguises: From Theory to Applications. Structure.

  • Trilles R, Beglov D, Chen Q, He H, Wireman R et al.. (2019). Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1. Journal of Medicinal Chemistry.

  • Ignatov M, Liu C, Alekseenko A, Sun Z, Padhorny D et al.. (2019). Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge. Journal of Computer-Aided Molecular Design.

  • Beglov D, Hall DR, Wakefield AE, Luo L, Allen KN et al.. (2018). Exploring the structural origins of cryptic sites on proteins. PNAS.           

  • Ignatov M, Kazennov A, Kozakov D. (2018). ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking. Journal of Molecular Biology.

  • Zarbafian S, Moghadasi M, Roshandelpoor A, Nan F, Li K et al.. (2018). Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes. Scientific Reports.              

  • Stasyk OG, Denega IO, Padhorny D, Dmytruk KV, Kozakov D et al.. (2018). Glucose regulation in the methylotrophic yeast Hansenula (Ogataea) polymorpha is mediated by a putative transceptor Gcr1. The International Journal of Biochemistry & Cell Biology.      

  • Vajda S, Beglov D, Wakefield AE, Egbert M, Whitty A. (2018). Cryptic binding sites on proteins: definition, detection, and druggability. Current Opinion in Chemical Biology.

  • Padhorny D, Hall DR, Mirzaei H, Mamonov AB, Moghadasi M et al.. (2018). Protein-ligand docking using FFT based sampling: D3R case study. Journal of Computer-Aided Molecular Design.

  • Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE et al.. (2017). New additions to the ClusPro server motivated by CAPRI. Proteins: Structure, Function, and Bioinformatics.

  • Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D et al.. (2017). The ClusPro web server for protein–protein docking.  Nature Protocols.

  • Yueh C, Hall DR, Xia B, Padhorny D, Kozakov D, Vajda S. (2017). ClusPro-DC: Dimer Classification by the Cluspro Server for Protein–Protein Docking. Journal of Molecular Biology.

  • Porter KA, Xia B, Beglov D, Bohnuud T, Alam N et al.. (2017). ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT.  Bioinformatics.

  • Alam N, Goldstein O, Xia B, Porter KA, Kozakov D, Schueler-Furman O et al.. (2017). High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. PLoS Computational Biology.

  • Bohnuud T, Jones G, Schueler-Furman O, Kozakov D. (2017). Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server. Methods in Molecular Biology.

  • Padhorny D, Kazennov A, Zerbe BS, Porter KA, Xia B et al.. (2016). Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds. Proceedings of the National Academy of Sciences.

  • Bohnuud T, Luo L, Wodak SJ, Bonvin AMJJ, Weng Z et al.. (2016). A benchmark testing ground for integrating homology modeling and protein docking. Proteins: Structure, Function, and Bioinformatics.

  • Whitty A, Zhong M, Viarengo L, Beglov D, Hall DR, Vajda S. (2016). Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs. Drug Discovery Today.

  • Mamonov AB, Moghadasi M, Mirzaei H, Zarbafian S, Grove LE et al.. (2016). Focused grid-based resampling for protein docking and mapping. Journal of Computational Chemistry.

  • Xia B, Vajda S, Kozakov D. (2016). Accounting for pairwise distance restraints in FFT-based protein–protein docking. Bioinformatics.               

  • Lensink MF, Velankar S, Kryshtafovych A, Huang S-Y, Schneidman-Duhovny D et al.. (2016). Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins: Structure, Function, and Bioinformatics.

  • Im W, Liang J, Olson A, Zhou H-X, Vajda S, Vakser IA. (2016). Challenges in structural approaches to cell modeling. Journal of Molecular Biology.

  • Vajda S, Whitty A, Kozakov D. (2015). Fragments and hot spots in drug discovery. Oncotarget.

  • Kozakov D, Grove LE, Hall DR, Bohnuud T, Mottarella SE et al.. (2015). The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. Nature Protocols.

  • Lukose V, Luo L, Kozakov D, Vajda S, Allen KN, Imperiali B. (2015). Conservation and covariance in small bacterial phosphoglycosyltransferases identify the functional catalytic core. Biochemistry. 

  • Hall DR, Kozakov D, Whitty A, Vajda S. (2015). Lessons from hot spot analysis for fragment-based drug discovery. Trends in Pharmacological Sciences. 

  • Kozakov D, Hall DR, Napoleon RL, Yueh C, Whitty A, Vajda S. (2015). New frontiers in druggability. Journal of Medicinal Chemistry.

  • Xia B, Mamonov A, Leysen S, Allen KN, Strelkov SV et al.. (2015). Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro. Journal of Computational Chemistry. 

  • Mirzaei H, Zarbafian S, Villar E, Mottarella S, Beglov D et al.. (2015). Energy Minimization on Manifolds for Docking Flexible Molecules. Journal of Chemical Theory and Computation.

  • Moghadasi M, Mirzaei H, Mamonov A, Vakili P, Vajda S et al.. (2015). The Impact of Side-Chain Packing on Protein Docking Refinement. Journal of Chemical Information and Modeling.

  • Kozakov D, Hall DR, Jehle S, Luo L, Ochiana SO et al.. (2015). Ligand deconstruction: Why some fragment binding positions are conserved and others are not. Proceedings of the National Academy of Sciences.

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