Vakser, Ilya A.

CAPRI: A Critical Assessment of PRedicted Interactions

Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J. E., Vajda, S., Vakser, I., & Wodak, S. J. (2003) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 703

Protein-Protein Docking: From Interaction to Interactome

Vakser, I. A. (2014) · Biophysical Journal

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 318

Identification of the Binding Site on Cytochrome P450 2B4 for Cytochrome b 5 and Cytochrome P450 Reductase

Bridges, A., Gruenke, L., Chang, Y.-T., Vakser, I. A., Loew, G., & Waskell, L. (1998) · Journal of Biological Chemistry

Metal-Catalyzed Oxygenation MechanismsPharmacogenetics and Drug Metabolism

Cited by 287

A systematic study of low-resolution recognition in protein-protein complexes

Vakser, I. A., Matar, O. G., & Lam, C. F. (1999) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 180

Templates are available to model nearly all complexes of structurally characterized proteins

Kundrotas, P. J., Zhu, Z., Janin, J., & Vakser, I. A. (2012) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 179

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

Low-resolution structural modeling of protein interactome

Vakser, I. A. (2013) · Current Opinion in Structural Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 62

Challenges in protein docking

Vakser, I. A. (2020) · Current Opinion in Structural Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 62

Natural language processing in text mining for structural modeling of protein complexes

Badal, V. D., Kundrotas, P. J., & Vakser, I. A. (2018) · BMC Bioinformatics

Biomedical Text Mining and OntologiesProtein Structure and Dynamics

Cited by 34

Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model

Anishchenko, I., Kundrotas, P. J., & Vakser, I. A. (2018) · Biophysical Journal

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 29

Computational feasibility of an exhaustive search of side-chain conformations in protein-protein docking

Dauzhenka, T., Kundrotas, P. J., & Vakser, I. A. (2018) · Journal of Computational Chemistry

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 17

How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking

Chakravarty, D., McElfresh, G., Kundrotas, P. J., & Vakser, I. A. (2020) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 13

Ensemble-based characterization of unbound and bound states on protein energy landscape

Ruvinsky, A. M., Kirys, T., Tuzikov, A. V., & Vakser, I. A. (2013) · Protein Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 9

Prediction of protein interactions is essential for studying biomolecular mechanisms

Vakser, I. (2023) · PROTEOMICS

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2

Prediction of protein interactions is essential for studying biomolecular mechanisms

Vakser, I. A. (2023) · PROTEOMICS

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2