ClusPro: an automated docking and discrimination method for the prediction of protein complexes

By Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho. Bioinform., 2004

918 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/467b52f2082462aa31dac07412acab1bb72017fa

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

1. Jeffrey J. Gray
2. Alexandre M. J. J. Bonvin
3. M. V. van Dijk
4. Sergey Lyskov
5. Haim J. Wolfson
6. Sjoerd Jacob de Vries
7. Nelly Andrusier
8. Ruth Nussinov

In Molecular Biology

1. Torsten Schwede
2. Andrej Sali
3. Yang Zhang
4. Ben M. Webb
5. David Baker
6. Jeffrey J. Gray
7. Andriy Kryshtafovych
8. Roland L. Dunbrack

Citations in the corpus

• FireDock: a web server for fast interaction refinement in molecular docking (2008, background): “ClusPro (22,23) can filter, cluster and rank docking solution candidates.”
• GRAMM-X public web server for protein–protein docking (2006, neutral): “edu/cluster/) (12), PatchDock/SymmDock (http://bioinfo3d.”
• Performance and its limits in rigid body protein-protein docking (2020, neutral): “The server performs three computational steps as follows: (1) rigid body docking using PIPER, (2) clustering the 1000 lowest energy docked structures using pairwise IRMSD as the distance measure (Comeau et al., 2004; Kozakov et al., 2005), and (3) refinement of the predicted complex structures locat”
• ClusPro: a fully automated algorithm for protein-protein docking (2004, methodology): “Using ClusPro’s (18) algorithm (Figure 1), the user has the option of selecting DOT (19,20) or ZDOCK (21,22) to perform rigid body docking, both of which are based on the fast Fourier”
• A Micropeptide Encoded by a Putative Long Non-coding RNA Regulates Muscle Performance (2015, neutral): “0 (Comeau et al., 2004).”
• The HADDOCK web server for data-driven biomolecular docking (2010, methodology): “A number of other docking servers have already been developed, such as ClusPro 17 , GRAMM-X 18 , PatchDock/FireDock 19–21 , Hex 22,23 and RosettaDock 24 .”
• FastContact: rapid estimate of contact and binding free energies (2005, methodology): “In the First Critical Assessment of PRedicted Interaction meeting, CAPRI (Janin et al ., 2003), computational scoring functions involved free energy-like terms adjusted by free parameters that optimized the discrimination of bound crystal structures (Fernández-Recio et al ., 2003; Gray et al .,…”