iATTRACT: Simultaneous global and local interface optimization for protein–protein docking refinement
CEM Schindler, SJ de Vries… - … : Structure, Function, and …, 2015 - Wiley Online Library
Protein‐protein interactions are abundant in the cell but to date structural data for a large
number of complexes is lacking. Computational docking methods can complement …
number of complexes is lacking. Computational docking methods can complement …
Rapid design of knowledge-based scoring potentials for enrichment of near-native geometries in protein-protein docking
Protein-protein docking protocols aim to predict the structures of protein-protein complexes
based on the structure of individual partners. Docking protocols usually include several …
based on the structure of individual partners. Docking protocols usually include several …
Protein-protein docking: From interaction to interactome
IA Vakser - Biophysical journal, 2014 - cell.com
The protein-protein docking problem is one of the focal points of activity in computational
biophysics and structural biology. The three-dimensional structure of a protein-protein …
biophysics and structural biology. The three-dimensional structure of a protein-protein …
LightDock: a new multi-scale approach to protein–protein docking
B Jiménez-García, J Roel-Touris… - …, 2018 - academic.oup.com
Motivation Computational prediction of protein–protein complex structure by docking can
provide structural and mechanistic insights for protein interactions of biomedical interest …
provide structural and mechanistic insights for protein interactions of biomedical interest …
Accounting for conformational changes during protein–protein docking
M Zacharias - Current opinion in structural biology, 2010 - Elsevier
Three-dimensional structures of only a small fraction of known protein–protein complexes
are currently known. Meanwhile, computational methods are of increasing importance to …
are currently known. Meanwhile, computational methods are of increasing importance to …
Protein docking by the interface structure similarity: how much structure is needed?
R Sinha, PJ Kundrotas, IA Vakser - PloS one, 2012 - journals.plos.org
The increasing availability of co-crystallized protein-protein complexes provides an
opportunity to use template-based modeling for protein-protein docking. Structure alignment …
opportunity to use template-based modeling for protein-protein docking. Structure alignment …
Identification of protein–protein interaction sites from docking energy landscapes
J Fernandez-Recio, M Totrov, R Abagyan - Journal of molecular biology, 2004 - Elsevier
Protein recognition is one of the most challenging and intriguing problems in structural
biology. Despite all the available structural, sequence and biophysical information about …
biology. Despite all the available structural, sequence and biophysical information about …
Protein–protein docking with backbone flexibility
Computational protein–protein docking methods currently can create models with atomic
accuracy for protein complexes provided that the conformational changes upon association …
accuracy for protein complexes provided that the conformational changes upon association …
Inherent limitations in protein–protein docking procedures
N Kowalsman, M Eisenstein - Bioinformatics, 2007 - academic.oup.com
Motivation: The limited success rate of protein–protein docking procedures is generally
attributed to structure differences between the bound and unbound states of the molecules …
attributed to structure differences between the bound and unbound states of the molecules …
FireDock: a web server for fast interaction refinement in molecular docking
E Mashiach, D Schneidman-Duhovny… - Nucleic acids …, 2008 - academic.oup.com
Structural details of protein–protein interactions are invaluable for understanding and
deciphering biological mechanisms. Computational docking methods aim to predict the …
deciphering biological mechanisms. Computational docking methods aim to predict the …