Dmytro Kozakov, Ph.D.

2007 Boston University, Boston, MA, United States 
Biomedical Engineering
"Dmytro Kozakov"
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Sandor Vajda grad student 2007 Boston University
 (Multistage approach to protein -protein interaction prediction.)


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Evangelos A. Coutsias collaborator (MathTree)
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Desta IT, Porter KA, Xia B, et al. (2020) Performance and Its Limits in Rigid Body Protein-Protein Docking. Structure (London, England : 1993)
Alekseenko A, Ignatov M, Jones G, et al. (2020) Protein-Protein and Protein-Peptide Docking with ClusPro Server. Methods in Molecular Biology (Clifton, N.J.). 2165: 157-174
Padhorny D, Porter KA, Ignatov M, et al. (2020) ClusPro in rounds 38-45 of CAPRI: Toward combining template-based methods with free docking. Proteins
Khramushin A, Marcu O, Alam N, et al. (2019) Modeling beta sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI Rounds 38-45. Proteins
Kotelnikov S, Alekseenko A, Liu C, et al. (2019) Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design
Alekseenko A, Kotelnikov S, Ignatov M, et al. (2019) ClusPro LigTBM: Automated Template-Based Small Molecule Docking. Journal of Molecular Biology
Zhong M, Lynch AJ, Muellers SN, et al. (2019) 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
Wang J, Alekseenko A, Kozakov D, et al. (2019) Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations. Frontiers in Molecular Biosciences. 6: 112
Lensink MF, Brysbaert G, Nadzirin N, et al. (2019) Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins
Porter KA, Padhorny D, Desta I, et al. (2019) Template-Based Modeling by ClusPro in CASP13 and the Potential for Using Co-evolutionary Information in Docking. Proteins
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