Prediction of protein-protein interactions by docking methods.

By Graham R. Smith, Michael J.E. Sternberg. Current Opinion in Structural Biology, 2002

480 citations recorded by the source corpus.

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

View Paper: https://www.semanticscholar.org/paper/626390db3ae27a471a160431d7d7b7f0f3baa7a6

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

In Materials Chemistry

In Molecular Biology

Citations in the corpus

Docking and scoring protein complexes: CAPRI 3rd Edition (2007, background): “With the rigid-body search algorithms, the core component of docking procedures, being well established,22,23 recent efforts have concentrated on other aspects that are key to successful docking predictions.”
Potential functions for hydrogen bonds in protein structure prediction and design. (2005, background): “…000012964.3D Proof by:Shankari QC by:Alakesan ProjectAcronym:bs:AIPC Volume:72002 U N C O R R E C T E D P R O O F reviews give a detailed account of the state of the art in this area (Camacho and Vajda, 2002; Halperin et al., 2002; Smith and Sternberg, 2002; Vajda and Camacho, 2004).”
Protein–protein interaction and quaternary structure (2008, background): “Protein–protein docking procedures have often been reviewed (Halperin et al. 2002 ; Smith & Sternberg, 2002 ; Marshall & Vakser, 2005 ; Gray, 2006 ; Wiehe et al. 2007).”
Exploiting sequence and structure homologs to identify protein–protein binding sites (2005, unknown): “16,17 Homology modeling 18 and multi-meric threading 19 approaches, which apply the knowledge learned from a known complex structure to the component (apo) homologs and examine the predicted contact residues using a speciﬁc potential function, are able to predict interaction partners of a protein…”
ZRANK: Reranking protein docking predictions with an optimized energy function (2007, background): “Several reviews have been published on protein–protein docking, including those by Smith and Sternberg, 2 and Halperin et al. 3 An overview of protein–protein interactions can be found in Jones and Thornton.”
ClusPro: an automated docking and discrimination method for the prediction of protein complexes (2004, background): “The challenge for predictive protein docking is to start with the coordinates of the unbound component molecules and to obtain a model for the bound complex (Camacho and Vajda, 2002; Halperin et al., 2002; Smith and Sternberg, 2002).”
Structural systems biology: modelling protein interactions (2006, background): “Classic 'docking' approaches attempt to find the best docked complex on the basis of shape or electrostatic complementarity between protein surface”
Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds (2016, unknown): “Thus, it is desirable to develop computational docking methods that, starting from the coordinates of two unbound component molecules deﬁned as receptor and ligand, respectively, are capable of providing a model of acceptable accuracy for the bound receptor-ligand complex [1, 2, 3, 4].”
Assessing predictions of protein–protein interaction: The CAPRI experiment (2005, methodology): “Docking algorithms developed in the years 1990–2000 have often been reviewed (Smith and Sternberg 2002; Halperin et al. 2002; Valencia and Pazos 2002; Wodak and Janin 2002).”
Integrating statistical pair potentials into protein complex prediction (2007, background): “2 Both identified three key ingredients: (1) representation of the system, (2) global conformational space search, and (3) reranking of top solutions based on a scoring function.”