FPDock: Protein-protein docking using flower pollination algorithm
Sign Up to like & getrecommendations! Published in 2021 at "Computational biology and chemistry"
DOI: 10.1016/j.compbiolchem.2021.107518
Abstract: Proteins play their vital role in biological systems through interaction and complex formation with other biological molecules. Indeed, abnormalities in the interaction patterns affect the proteins' structure and have detrimental effects on living organisms. Research… read more here.
Keywords: protein; protein docking; protein protein; flower pollination ... See more keywords
Advances to tackle backbone flexibility in protein docking.
Sign Up to like & getrecommendations! Published in 2020 at "Current opinion in structural biology"
DOI: 10.1016/j.sbi.2020.11.011
Abstract: Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were submitted in less than 20%… read more here.
Keywords: tackle backbone; advances tackle; flexibility; protein docking ... See more keywords
Protein Docking Using a Single Representation for Protein Surface, Electrostatics, and Local Dynamics
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.9b00474
Abstract: Predicting the assembly of multiple proteins into specific complexes is critical to understanding their biological function in an organism and thus the design of drugs to address their malfunction. Proteins are flexible molecules, which inherently… read more here.
Keywords: protein; protein docking; electrostatics; protein surface ... See more keywords
The ClusPro web server for protein–protein docking
Sign Up to like & getrecommendations! Published in 2017 at "Nature Protocols"
DOI: 10.1038/nprot.2016.169
Abstract: The ClusPro server (https://cluspro.org) is a widely used tool for protein–protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also… read more here.
Keywords: protein; cluspro web; protein docking; energy ... See more keywords
Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes
Sign Up to like & getrecommendations! Published in 2018 at "Scientific Reports"
DOI: 10.1038/s41598-018-23982-3
Abstract: We propose a novel stochastic global optimization algorithm with applications to the refinement stage of protein docking prediction methods. Our approach can process conformations sampled from multiple clusters, each roughly corresponding to a different binding… read more here.
Keywords: protein docking; docking refinement; subspace; refinement convex ... See more keywords
InterPep2: global peptide–protein docking using interaction surface templates
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa005
Abstract: Abstract Motivation Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is… read more here.
Keywords: protein; peptide protein; protein docking; interpep2 global ... See more keywords
TRScore: a three-dimensional RepVGG-based scoring method for ranking protein docking models.
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac120
Abstract: MOTIVATION Protein-protein interactions (PPI) play important roles in cellular activities. Due to the technical difficulty and high cost of experimental methods, there are considerable interests towards the development of computational approaches, such as protein docking,… read more here.
Keywords: protein protein; method ranking; protein docking; based scoring ... See more keywords
LightDock: a new multi-scale approach to protein–protein docking
Sign Up to like & getrecommendations! Published in 2018 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx555
Abstract: Motivation Computational prediction of protein-protein complex structure by docking can provide structural and mechanistic insights for protein interactions of biomedical interest. However, current methods struggle with difficult cases, such as those involving flexible proteins, low-affinity… read more here.
Keywords: protein; protein docking; new multi; protein protein ... See more keywords
PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network.
Sign Up to like & getrecommendations! Published in 2023 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2023.3279019
Abstract: Protein-protein interactions (PPIs) play essential roles in many vital movements and the determination of protein complex structure is helpful to discover the mechanism of PPI. Protein-protein docking is being developed to model the structure of… read more here.
Keywords: point cloud; network; protein docking; protein ... See more keywords
AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking
Sign Up to like & getrecommendations! Published in 2017 at "BMC Bioinformatics"
DOI: 10.1186/s12859-017-1628-6
Abstract: BackgroundComputational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the near-native poses of the protein-protein complex in… read more here.
Keywords: protein; native poses; protein docking; ankyrin protein ... See more keywords
Pushing the accuracy limit of shape complementarity for protein-protein docking
Sign Up to like & getrecommendations! Published in 2019 at "BMC Bioinformatics"
DOI: 10.1186/s12859-019-3270-y
Abstract: Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role in protein-protein docking. Despite significant progresses, shape representation… read more here.
Keywords: protein; shape complementarity; protein docking; protein protein ... See more keywords