Dima Kozakov

35 papers Journal 27Unranked 8
YearRankTypeTitle / Venue / Authors
2026 J jnl
CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2.
J. Chem. Inf. Model.
Oleksandra Herasymenko, Madhushika Silva, Galen J. Correy, Abd Al-Aziz A. Abu-Saleh, Suzanne Ackloo, Cheryl H. Arrowsmith, Alan Ashworth, Fuqiang Ban, Hartmut Beck, Kevin P. Bishop, Hugo J. Bohórquez, Albina Bolotokova, Marko Breznik, Irene Chau, Yu Chen, Artem Cherkasov, Wim Dehaen, Dennis Della Corte, Katrin Denzinger, Niklas Piet Doering, Kristina Edfeldt, Aled M. Edwards, Darren Fayne, Francesco Gentile, Elisa Gibson, Ozan Gökdemir, Anders Gunnarsson, Judith Guenther, John J. Irwin, Jan Halborg Jensen, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Ashley Hutchinson, Shubhangi Kandwal, Andrea Karlova, Kushal Koirala, Sergei Kotelnikov, Dima Kozakov, Juyong Lee, Soowon Lee, Uta F. Lessel, Sijie Liu, Xuefeng Liu, Peter Loppnau, Jens Meiler, Rocco Moretti, Yurii S. Moroz, Charuvaka Muvva, Tudor I. Oprea, Brooks Paige, Amit Pandit, Keunwan Park, Gennady Poda, Mykola V. Protopopov, Vera Pütter, Rahul Ravichandran, Didier Rognan, Edina Rosta, Yogesh Sabnis, Thomas Scott, Almagul Seitova, Purshotam Sharma, François Sindt, Minghu Song, Casper Steinmann, Rick Stevens, Valerij Talagayev, Valentyna V. Tararina, Olga O. Tarkhanova, Damon Tingey, John F. Trant, Dakota Treleaven, Alexander Tropsha, W. Patrick Walters, Jude Wells, Yvonne Westermaier, Gerhard Wolber, Lars Wortmann, Shuangjia Zheng, James S. Fraser, Matthieu Schapira
2025 J jnl
Impact of Protein Conformational Diversity on Structure-Based Prediction of Druggability.
J. Chem. Inf. Model.
Ayse A. Bekar-Cesaretli, Shray Vats, Adrian Whitty, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda
2024 J jnl
Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2.
J. Chem. Inf. Model.
Ayse A. Bekar-Cesaretli, Omeir Khan, Thu Nguyen, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda
2024 J jnl
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites.
J. Chem. Inf. Model.
Omeir Khan, George Jones, Maria Lazou, Diane Joseph-McCarthy, Dima Kozakov, Dmitri Beglov, Sandor Vajda
2023 J jnl
Improved prediction of MHC-peptide binding using protein language models.
Frontiers Bioinform.
Nasser Hashemi, Boran Hao, Mikhail Ignatov, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, Dima Kozakov
2023 — conf
Numerically stable algorithm for Inverse Kinematics of 6R problem and its applications to macrocycles.
BCB
Xin Cao, Mikhail Ignatov, George Jones, Sara N. Pollock, Evangelos A. Coutsias, Dima Kozakov
2022 J jnl
Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors.
J. Chem. Inf. Model.
Amanda E. Wakefield, Dávid Bajusz, Dima Kozakov, György M. Keserü, Sandor Vajda
2020 J jnl
Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery.
J. Chem. Inf. Model.
Amanda E. Wakefield, Christine Yueh, Dmitri Beglov, Marcelo Santos Castilho, Dima Kozakov, György M. Keserü, Adrian Whitty, Sandor Vajda
2020 J jnl
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.
J. Comput. Aided Mol. Des.
Sergei Kotelnikov, Andrey Alekseenko, Cong Liu, Mikhail Ignatov, Dzmitry Padhorny, Emiliano Brini, Mark Lukin, Evangelos A. Coutsias, Ken A. Dill, Dima Kozakov
2019 J jnl
Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge.
J. Comput. Aided Mol. Des.
Mikhail Ignatov, Cong Liu, Andrey Alekseenko, Zhuyezi Sun, Dzmitry Padhorny, Sergei Kotelnikov, Andrey M. Kazennov, Ivan Grebenkin, Yaroslav Kholodov, Istvan Kolosvari, Alberto Pérez, Ken A. Dill, Dima Kozakov
2018 J jnl
Protein-ligand docking using FFT based sampling: D3R case study.
J. Comput. Aided Mol. Des.
Dzmitry Padhorny, David R. Hall, Hanieh Mirzaei, Artem B. Mamonov, Mohammad Moghadasi, Andrey Alekseenko, Dmitri Beglov, Dima Kozakov
2017 J jnl
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT.
Bioinform.
Kathryn A. Porter, Bing Xia, Dmitri Beglov, Tanggis Bohnuud, Nawsad Alam, Ora Schueler-Furman, Dima Kozakov
2017 J jnl
High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock.
PLoS Comput. Biol.
Nawsad Alam, Oriel Goldstein, Bing Xia, Kathryn A. Porter, Dima Kozakov, Ora Schueler-Furman
2016 J jnl
Accounting for pairwise distance restraints in FFT-based protein-protein docking.
Bioinform.
Bing Xia, Sandor Vajda, Dima Kozakov
2016 J jnl
Focused grid-based resampling for protein docking and mapping.
J. Comput. Chem.
Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov
2015 J jnl
Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro.
J. Comput. Chem.
Bing Xia, Artem B. Mamonov, Seppe Leysen, Karen N. Allen, Sergei V. Strelkov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov
2015 J jnl
The Impact of Side-Chain Packing on Protein Docking Refinement.
J. Chem. Inf. Model.
Mohammad Moghadasi, Hanieh Mirzaei, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis, Dima Kozakov
2014 — conf
A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking.
CDC
Feng Nan, Mohammad Moghadasi, Pirooz Vakili, Sandor Vajda, Dima Kozakov, Ioannis Ch. Paschalidis
2014 J jnl
Docking Server for the Identification of Heparin Binding Sites on Proteins.
J. Chem. Inf. Model.
Scott E. Mottarella, Dmitri Beglov, Natalia Beglova, Matthew A. Nugent, Dima Kozakov, Sandor Vajda
2014 J jnl
Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces.
PLoS Comput. Biol.
Tanggis Bohnuud, Dima Kozakov, Sandor Vajda
2014 — conf
Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach.
CDC
Pirooz Vakili, Hanieh Mirzaei, Shahrooz Zarbafian, Ioannis Ch. Paschalidis, Dima Kozakov, Sandor Vajda
2013 — conf
A new distributed algorithm for side-chain positioning in the process of protein docking.
CDC
Mohammad Moghadasi, Dima Kozakov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis
2013 J jnl
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.
Bioinform.
Laurie E. Grove, David R. Hall, Dmitri Beglov, Sandor Vajda, Dima Kozakov
2013 — conf
Flexible refinement of protein-ligand docking on manifolds.
CDC
Hanieh Mirzaei, Elizabeth A. Villar, Scott E. Mottarella, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov, Pirooz Vakili
2012 — conf
A message passing approach to Side Chain Positioning with applications in protein docking refinement.
CDC
Mohammad Moghadasi, Dima Kozakov, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis
2012 — conf
A new approach to rigid body minimization with application to molecular docking.
CDC
Hanieh Mirzaei, Dima Kozakov, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Pirooz Vakili
2012 J jnl
Application of asymmetric statistical potentials to antibody-protein docking.
Bioinform.
Ryan Brenke, David R. Hall, Gwo-Yu Chuang, Stephen R. Comeau, Tanggis Bohnuud, Dmitri Beglov, Ora Schueler-Furman, Sandor Vajda, Dima Kozakov
2012 J jnl
FTMAP: extended protein mapping with user-selected probe molecules.
Nucleic Acids Res.
Chi-Ho Ngan, Tanggis Bohnuud, Scott E. Mottarella, Dmitri Beglov, Elizabeth A. Villar, David R. Hall, Dima Kozakov, Sandor Vajda
2012 J jnl
FTSite: high accuracy detection of ligand binding sites on unbound protein structures.
Bioinform.
Chi-Ho Ngan, David R. Hall, Brandon S. Zerbe, Laurie E. Grove, Dima Kozakov, Sandor Vajda
2012 J jnl
Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery.
J. Chem. Inf. Model.
David R. Hall, Chi-Ho Ngan, Brandon S. Zerbe, Dima Kozakov, Sandor Vajda
2012 J jnl
Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces.
J. Chem. Inf. Model.
Brandon S. Zerbe, David R. Hall, Sandor Vajda, Adrian Whitty, Dima Kozakov
2009 J jnl
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase.
J. Comput. Aided Mol. Des.
Melissa R. Landon, Raquel L. Lieberman, Quyen Q. Hoang, Shulin Ju, Jose M. M. Caaveiro, Susan D. Orwig, Dima Kozakov, Ryan Brenke, Gwo-Yu Chuang, Dmitri Beglov, Sandor Vajda, Gregory A. Petsko, Dagmar Ringe
2009 J jnl
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques.
Bioinform.
Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David R. Hall, Melissa R. Landon, Carla Mattos, Sandor Vajda
2008 J jnl
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.
Bioinform.
David W. Ritchie, Dima Kozakov, Sandor Vajda
2008 — conf
Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand Docking.
BIOCOMP
Taner Kaya, Dima Kozakov, Sandor Vajda