Protein-protein docking: from interaction to interactome.

By Ilya A. Vakser. 2014

288 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

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Citations in the corpus

Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XIV (2021, methodology): “groups used classical docking methods in which a search is made for sterically and electrostatically complementary surfaces.(27) A number of groups have now augmented these with the prediction in interface residue–residue contacts, often employing deep-learning methods, for example,(22) producing so”
Machine Learning in Drug Discovery: A Review (2021, background): “If the chance of two interactive protein structures is vacant then it makes it easy for predicting the PPI interface (Vakser 2014) where it mainly relies on complementarity rules of protein-protein docking (Chen et al.”
The HDOCK server for integrated protein–protein docking (2020, background): “Optional buttons on the right (3) can control the NGL viewer to visualize the binding model on the left (4).”
Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes (2020, background): “Determining structures of protein complexes experimentally is often difficult and time-consuming, placing a premium on computational structure prediction.(2) Unfortunately, computational structure prediction for protein complexes has also proven difficult—much more so than for individual proteins.”
Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets (2017, background): “Often, a change in conformation from the unbound to the bound state forms the basis of the protein’s specificity and function in its interaction (Chu et al. , 2013; Hwang et al. , 2010; Vakser, 2014; increasing the degrees of freedom to be sampled.”
HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, background): “Therefore, determination of their complex structures is critical to understand the underlying molecular mechanisms of crucial biological processes (1) and even design compounds that interfere with PPIs with pharmaceutical significance (2).”
Modeling complexes of modeled proteins (2017, background): “FSC-score5 jStempl\Smodelj jStempl[Smodelj ; (3)”
Application of docking methodologies to modeled proteins (2020, background): “6 Along with the robustness of the alignment protocol, the success of comparative docking is determined by the size and diversity of the template library.”
Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking (2021, background): “Experimentally determining structures of protein complexes is often expensive and time-consuming, rendering a premium on computational methods (Vakser, 2014).”
Dockground: A comprehensive data resource for modeling of protein complexes (2018, methodology): “16 In this paper, we present for the first time the most recent docking benchmark set 4.”