Kozakov, Dima

PIPER: An FFT‐based protein docking program with pairwise potentials

Kozakov, D., Brenke, R., Comeau, S. R., & Vajda, S. (2006) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 865

Allostery in Its Many Disguises: From Theory to Applications

Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., et al. (2019) · Structure

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 404

A critical overview of computational approaches employed for COVID-19 drug discovery

Muratov, E. N., Amaro, R., Andrade, C. H., Brown, N., Ekins, S., Fourches, D., Isayev, O., Kozakov, D., Medina-Franco, J. L., Merz, K. M., et al. (2021) · Chemical Society Reviews

Computational Drug Discovery MethodsSARS-CoV-2 and COVID-19 Research

Cited by 206

Blind prediction of homo- and hetero-protein complexes: the CASP13-CAPRI experiment

Lensink, M. F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Gerguri, T., Bates, P. A., Laine, E., Carbone, A., Grudinin, S., et al. (2019) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 122

Improved Docking of Protein Models by a Combination of Alphafold2 and ClusPro

Ghani, U., Desta, I., Jindal, A., Khan, O., Jones, G., Hashemi, N., Kotelnikov, S., Padhorny, D., Vajda, S., & Kozakov, D. (2021) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 68

ClusPro-DC: dimer classification by the Cluspro server for protein–protein docking

Yueh, C., Hall, D. R., Xia, B., Padhorny, D., Kozakov, D., & Vajda, S. (2017) · Journal of Molecular Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 53

Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-κB Essential Modulator/IKKβ Protein–Protein Interface

Golden, M. S., Cote, S. M., Sayeg, M., Zerbe, B. S., Villar, E. A., Beglov, D., Sazinsky, S. L., Georgiadis, R. M., Vajda, S., Kozakov, D., et al. (2013) · Journal of the American Chemical Society

NF-κB Signaling PathwaysComputational Drug Discovery Methods

Cited by 47

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces

Bohnuud, T., Kozakov, D., & Vajda, S. (2014) · PLoS Computational Biology

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 27

Improved Predictions of MHC-Peptide Binding using Protein Language Models

Hashemi, N., Hao, B., Ignatov, M., Paschalidis, I., Vakili, P., Vajda, S., & Kozakov, D. (2022) · Frontiers in Bioinformatics

vaccines and immunoinformatics approachesMachine Learning in Bioinformatics

Cited by 25

Improved prediction of MHC-peptide binding using protein language models

Hashemi, N., Hao, B., Ignatov, M., Paschalidis, I. C., Vakili, P., Vajda, S., & Kozakov, D. (2023) · Frontiers in Bioinformatics

vaccines and immunoinformatics approachesMachine Learning in Bioinformatics

Cited by 25

MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction

Glukhov, E., Kalitin, D., Stepanenko, D., Zhu, Y., Nguyen, T., Jones, G., Simmerling, C., Mitchell, J. C., Vajda, S., Dill, K. A., et al. (2023) · Biophysical Journal

vaccines and immunoinformatics approachesProtein Structure and Dynamics

Cited by 22

Assessing the binding properties of CASP14 targets and models

Egbert, M., Ghani, U., Ashizawa, R., Kotelnikov, S., Nguyen, T., Desta, I., Hashemi, N., Padhorny, D., Kozakov, D., & Vajda, S. (2021) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 10