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Dzmitry Padhorny
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The ClusPro web server for protein–protein docking
D Kozakov, DR Hall, B Xia, KA Porter, D Padhorny, C Yueh, D Beglov, ...
Nature protocols 12 (2), 255-278, 2017
23272017
Allostery in its many disguises: from theory to applications
SJ Wodak, E Paci, NV Dokholyan, IN Berezovsky, A Horovitz, J Li, ...
Structure 27 (4), 566-578, 2019
2982019
Actionable cytopathogenic host responses of human alveolar type 2 cells to SARS-CoV-2
RM Hekman, AJ Hume, RK Goel, KM Abo, J Huang, BC Blum, RB Werder, ...
Molecular cell 81 (1), 212, 2021
1112021
Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment
MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, ...
Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019
1112019
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
MF Lensink, G Brysbaert, T Mauri, N Nadzirin, S Velankar, RAG Chaleil, ...
Proteins: Structure, Function, and Bioinformatics 89 (12), 1800-1823, 2021
762021
Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds
D Padhorny, A Kazennov, BS Zerbe, KA Porter, B Xia, SE Mottarella, ...
Proceedings of the National Academy of Sciences 113 (30), E4286-E4293, 2016
672016
Improved docking of protein models by a combination of alphafold2 and cluspro
U Ghani, I Desta, A Jindal, O Khan, G Jones, N Hashemi, S Kotelnikov, ...
BioRxiv, 2021.09. 07.459290, 2021
592021
Protein folds vs. protein folding: Differing questions, different challenges
SJ Chen, M Hassan, RL Jernigan, K Jia, D Kihara, A Kloczkowski, ...
Proceedings of the National Academy of Sciences 120 (1), e2214423119, 2023
442023
ClusPro-DC: Dimer classification by the CLUSPRO server for protein–protein docking
C Yueh, DR Hall, B Xia, D Padhorny, D Kozakov, S Vajda
Journal of molecular biology 429 (3), 372-381, 2017
402017
Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery
PC Havugimana, RK Goel, S Phanse, A Youssef, D Padhorny, ...
Nature communications 13 (1), 4043, 2022
272022
Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking
KA Porter, D Padhorny, I Desta, M Ignatov, D Beglov, S Kotelnikov, Z Sun, ...
Proteins: Structure, Function, and Bioinformatics 87 (12), 1241-1248, 2019
192019
Protein–ligand docking using FFT based sampling: D3R case study
D Padhorny, DR Hall, H Mirzaei, AB Mamonov, M Moghadasi, ...
Journal of computer-aided molecular design 32, 225-230, 2018
192018
Monte Carlo on the manifold and MD refinement for binding pose prediction of protein–ligand complexes: 2017 D3R Grand Challenge
M Ignatov, C Liu, A Alekseenko, Z Sun, D Padhorny, S Kotelnikov, ...
Journal of computer-aided molecular design 33, 119-127, 2019
172019
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4
S Kotelnikov, A Alekseenko, C Liu, M Ignatov, D Padhorny, E Brini, ...
Journal of computer-aided molecular design 34, 179-189, 2020
152020
Assessing the binding properties of CASP14 targets and models
M Egbert, U Ghani, R Ashizawa, S Kotelnikov, T Nguyen, I Desta, ...
Proteins: Structure, Function, and Bioinformatics 89 (12), 1922-1939, 2021
132021
Impact of AlphaFold on structure prediction of protein complexes: the CASP15‐CAPRI experiment
MF Lensink, G Brysbaert, N Raouraoua, PA Bates, M Giulini, RV Honorato, ...
Proteins: Structure, Function, and Bioinformatics 91 (12), 1658-1683, 2023
122023
Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45
A Khramushin, O Marcu, N Alam, O Shimony, D Padhorny, E Brini, KA Dill, ...
Proteins: Structure, Function, and Bioinformatics 88 (8), 1037-1049, 2020
112020
ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking
D Padhorny, KA Porter, M Ignatov, A Alekseenko, D Beglov, S Kotelnikov, ...
Proteins: Structure, Function, and Bioinformatics 88 (8), 1082-1090, 2020
82020
Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT
I Paul, D Bolzan, A Youssef, KA Gagnon, H Hook, G Karemore, ...
Nature communications 14 (1), 688, 2023
72023
Side-chain packing using SE (3)-transformer
A Jindal, S Kotelnikov, D Padhorny, D Kozakov, Y Zhu, R Chowdhury, ...
PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022, 46-55, 2021
52021
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