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ORCIDDima Kozakov
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2020 – today
- 2024
[j25]Ayse A. Bekar-Cesaretli
, Omeir Khan, Thu Nguyen, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda:
Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. J. Chem. Inf. Model. 64(3): 960-973 (2024)- [j24]Omeir Khan, George Jones, Maria Lazou, Diane Joseph-McCarthy, Dima Kozakov, Dmitri Beglov, Sandor Vajda:
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. J. Chem. Inf. Model. 64(6): 2084-2100 (2024) - 2023
- [j23]Nasser Hashemi, Boran Hao, Mikhail Ignatov, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, Dima Kozakov:
Improved prediction of MHC-peptide binding using protein language models. Frontiers Bioinform. 3 (2023) - [c8]Xin Cao, Mikhail Ignatov, George Jones, Sara N. Pollock, Evangelos A. Coutsias, Dima Kozakov:
Numerically stable algorithm for Inverse Kinematics of 6R problem and its applications to macrocycles. BCB 2023: 84:1 - 2022
- [j22]Amanda E. Wakefield, Dávid Bajusz, Dima Kozakov, György M. Keserü, Sandor Vajda:
Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. J. Chem. Inf. Model. 62(20): 4937-4954 (2022) - 2020
- [j21]Sergei Kotelnikov, Andrey Alekseenko, Cong Liu, Mikhail Ignatov, Dzmitry Padhorny, Emiliano Brini, Mark Lukin, Evangelos A. Coutsias, Ken A. Dill, Dima Kozakov:
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. J. Comput. Aided Mol. Des. 34(2): 179-189 (2020) - [j20]Amanda E. Wakefield, Christine Yueh, Dmitri Beglov, Marcelo Santos Castilho, Dima Kozakov, György M. Keserü, Adrian Whitty, Sandor Vajda:
Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. J. Chem. Inf. Model. 60(12): 6612-6623 (2020)
2010 – 2019
- 2019
- [j19]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:
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. 33(1): 119-127 (2019) - 2018
- [j18]Dzmitry Padhorny, David R. Hall, Hanieh Mirzaei, Artem B. Mamonov, Mohammad Moghadasi, Andrey Alekseenko, Dmitri Beglov, Dima Kozakov:
Protein-ligand docking using FFT based sampling: D3R case study. J. Comput. Aided Mol. Des. 32(1): 225-230 (2018) - 2017
- [j17]Kathryn A. Porter, Bing Xia, Dmitri Beglov, Tanggis Bohnuud, Nawsad Alam, Ora Schueler-Furman, Dima Kozakov:
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. Bioinform. 33(20): 3299-3301 (2017) - [j16]Nawsad Alam, Oriel Goldstein, Bing Xia, Kathryn A. Porter, Dima Kozakov, Ora Schueler-Furman:
High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. PLoS Comput. Biol. 13(12) (2017) - 2016
- [j15]Bing Xia, Sandor Vajda, Dima Kozakov:
Accounting for pairwise distance restraints in FFT-based protein-protein docking. Bioinform. 32(21): 3342-3344 (2016) - [j14]Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov:
Focused grid-based resampling for protein docking and mapping. J. Comput. Chem. 37(11): 961-970 (2016) - 2015
- [j13]Bing Xia, Artem B. Mamonov, Seppe Leysen, Karen N. Allen, Sergei V. Strelkov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov:
Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro. J. Comput. Chem. 36(20): 1568-1572 (2015) - [j12]Mohammad Moghadasi, Hanieh Mirzaei, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis, Dima Kozakov:
The Impact of Side-Chain Packing on Protein Docking Refinement. J. Chem. Inf. Model. 55(4): 872-881 (2015) - 2014
- [j11]Scott E. Mottarella, Dmitri Beglov, Natalia Beglova, Matthew A. Nugent, Dima Kozakov, Sandor Vajda:
Docking Server for the Identification of Heparin Binding Sites on Proteins. J. Chem. Inf. Model. 54(7): 2068-2078 (2014) - [j10]Tanggis Bohnuud, Dima Kozakov, Sandor Vajda:
Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces. PLoS Comput. Biol. 10(10) (2014) - [c7]Feng Nan, Mohammad Moghadasi, Pirooz Vakili, Sandor Vajda, Dima Kozakov, Ioannis Ch. Paschalidis:
A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking. CDC 2014: 4623-4628 - [c6]Pirooz Vakili, Hanieh Mirzaei, Shahrooz Zarbafian, Ioannis Ch. Paschalidis, Dima Kozakov, Sandor Vajda:
Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach. CDC 2014: 5825-5830 - 2013
- [j9]Laurie E. Grove, David R. Hall, Dmitri Beglov, Sandor Vajda, Dima Kozakov:
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinform. 29(9): 1218-1219 (2013) - [c5]Mohammad Moghadasi, Dima Kozakov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis:
A new distributed algorithm for side-chain positioning in the process of protein docking. CDC 2013: 739-744 - [c4]Hanieh Mirzaei, Elizabeth A. Villar, Scott E. Mottarella, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov, Pirooz Vakili:
Flexible refinement of protein-ligand docking on manifolds. CDC 2013: 1392-1397 - 2012
- [j8]Chi-Ho Ngan, David R. Hall, Brandon S. Zerbe, Laurie E. Grove, Dima Kozakov, Sandor Vajda:
FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinform. 28(2): 286-287 (2012) - [j7]Ryan Brenke, David R. Hall, Gwo-Yu Chuang, Stephen R. Comeau, Tanggis Bohnuud, Dmitri Beglov, Ora Schueler-Furman, Sandor Vajda, Dima Kozakov:
Application of asymmetric statistical potentials to antibody-protein docking. Bioinform. 28(20): 2608-2614 (2012) - [j6]David R. Hall, Chi-Ho Ngan, Brandon S. Zerbe, Dima Kozakov, Sandor Vajda:
Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. J. Chem. Inf. Model. 52(1): 199-209 (2012) - [j5]Brandon S. Zerbe, David R. Hall, Sandor Vajda, Adrian Whitty, Dima Kozakov:
Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces. J. Chem. Inf. Model. 52(8): 2236-2244 (2012) - [j4]Chi-Ho Ngan, Tanggis Bohnuud, Scott E. Mottarella, Dmitri Beglov, Elizabeth A. Villar, David R. Hall, Dima Kozakov, Sandor Vajda:
FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Res. 40(Web-Server-Issue): 271-275 (2012) - [c3]Mohammad Moghadasi, Dima Kozakov, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis:
A message passing approach to Side Chain Positioning with applications in protein docking refinement. CDC 2012: 2310-2315 - [c2]Hanieh Mirzaei, Dima Kozakov, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Pirooz Vakili:
A new approach to rigid body minimization with application to molecular docking. CDC 2012: 2983-2988
2000 – 2009
- 2009
- [j3]Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David R. Hall, Melissa R. Landon, Carla Mattos, Sandor Vajda:
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinform. 25(5): 621-627 (2009) - [j2]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:
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J. Comput. Aided Mol. Des. 23(8): 491-500 (2009) - 2008
- [j1]David W. Ritchie, Dima Kozakov, Sandor Vajda:
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinform. 24(17): 1865-1873 (2008) - [c1]Taner Kaya, Dima Kozakov, Sandor Vajda:
Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand Docking. BIOCOMP 2008: 1028-1032
Coauthor Index
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