DOI: 10.1016/j.sbi.2009.02.008. Convergence and combination of methods in protein

Convergence and combination of methods in protein–protein docking

10.1016/j.sbi.2009.02.008

Crossref journal-article

Elsevier BV

Current Opinion in Structural Biology (78)

Bibliography

Vajda, S., & Kozakov, D. (2009). Convergence and combination of methods in proteinâprotein docking. Current Opinion in Structural Biology, 19(2), 164â170.

Authors 2

Sandor Vajda (first)
Dima Kozakov (additional)

References 40 Referenced 179

10.2174/138920308783565741 / Curr Protein Pept Sci / Recent progress and future directions in protein–protein docking by Ritchie (2008)
10.1002/prot.22170 / Proteins / Principles of flexible protein–protein docking by Andrusier (2008)
10.1002/prot.10381 / Proteins / CAPRI: a Critical Assessment of PRedicted Interactions by Janin (2003)
10.1002/prot.10393 / Proteins / Assessment of blind predictions of protein–protein interactions: current status of docking methods by Mendez (2003)
10.1002/prot.20551 / Proteins / Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures by Mendez (2005)
10.1002/prot.21804 / Proteins / Docking and scoring protein complexes: CAPRI 3rd Edition by Lensink (2007)
10.1002/prot.21747 / Proteins / The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI by Wiehe (2007)
10.1002/prot.21754 / Proteins / Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI by Shen (2007)
10.1002/prot.21795 / Proteins / ClusPro: performance in CAPRI rounds 6–11 and the new server by Comeau (2007)
10.1002/prot.20575 / Proteins / Improving CAPRI predictions: optimized desolvation for rigid-body docking by Fernández-Recio (2005)
10.1002/prot.21684 / Proteins / RosettaDock in CAPRI rounds 6–12 by Wang (2007)
10.1002/prot.21759 / Proteins / Automatic prediction of protein interactions with large scale motion by Schneidman-Duhovny (2007)
10.1093/nar/gkn186 / Nucleic Acids Res / FireDock: a web server for fast interaction refinement in molecular docking by Mashiach (2008)
10.1093/bioinformatics/btl524 / Bioinformatics / Inherent limitations in protein–protein docking procedures by Kowalsman (2007)
10.1002/prot.21723 / Proteins / HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets by de Vries (2007)
10.1002/prot.22106 / Proteins / Protein–protein docking benchmark version 3.0 by Hwang (2008)
10.1002/prot.20554 / Proteins / Classification of protein complexes based on docking difficulty by Vajda (2005)
10.1002/prot.20562 / Proteins / Geometry-based flexible and symmetric protein docking by Schneidman-Duhovny (2005)
10.1073/pnas.89.6.2195 / Proc Natl Acad Sci U S A / Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques by Katchalski-Katzir (1992)
10.1002/prot.21117 / Proteins / PIPER: an FFT-based protein docking program with pairwise potentials by Kozakov (2006)
10.1002/prot.21502 / Proteins / Integrating statistical pair potentials into protein complex prediction by Mintseris (2007)
10.1002/prot.10383 / Proteins / ICM-DISCO docking by global energy optimization with fully flexible side-chains by Fernandez-Recio (2003)
10.1016/S0022-2836(03)00670-3 / J Mol Biol / Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations by Gray (2003)
10.1016/j.jmb.2007.07.050 / J Mol Biol / Protein–protein docking with backbone flexibility by Wang (2007)
10.1021/ja026939x / J Am Chem Soc / HADDOCK: a protein–protein docking approach based on biochemical and/or biophysical information by Dominguez (2003)
10.1093/bioinformatics/btg371 / Bioinformatics / ClusPro: an automated docking and discrimination method for the prediction of protein complexes by Comeau (2004)
10.1529/biophysj.104.058768 / Biophys J / Optimal clustering for detecting near-native conformations in protein docking by Kozakov (2005)
10.1002/prot.21442 / Proteins / Identification of near-native structures by clustering protein docking conformations by Lorenzen (2007)
10.1002/prot.21665 / Proteins / Large-scale characteristics of the energy landscape in protein–protein interactions by O’Toole (2008)
10.1016/j.jmb.2008.05.042 / J Mol Biol / Conformer selection and induced fit in flexible backbone protein–protein docking using computational and NMR ensembles by Chaudhury (2008)
10.1109/TAC.2007.894518 / IEEE Trans Autom Control / A semi-definite programming-based underestimation method for global optimization in molecular docking by Paschalidis (2007)
10.1371/journal.pcbi.1000191 / PLoS Comput Biol / Protein docking by the underestimation of free energy funnels in the space of encounter complexes by Shen (2008)
10.1016/j.str.2007.11.013 / Structure / Funnel hunting in a rough terrain. learning and discriminating native energy funnels by London (2008)
10.1002/prot.21997 / Proteins / Discrimination of near-native structures in protein–protein docking by testing the stability of local minima by Kozakov (2008)
10.1002/prot.21920 / Proteins / A combination of rescoring and refinement significantly improves protein docking performance by Pierce (2008)
10.1110/ps.072847207 / Protein Sci / Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization by Lorenzen (2007)
10.1021/ja042260c / J Am Chem Soc / Representing receptor flexibility in ligand docking through relevant normal modes by Cavasotto (2005)
10.1093/bioinformatics/btm014 / Bioinformatics / DFprot: a webtool for predicting local chain deformability by Garzón (2007)
10.1073/pnas.0802496105 / Proc Natl Acad Sci U S A / Insights into protein flexibility: the relationship between normal modes and conformational change upon protein–protein docking by Dobbins (2008)
10.1002/prot.21613 / Proteins / HingeProt: automated prediction of hinges in protein structures by Emekli (2008)

Dates

Type	When
Created	16 years, 5 months ago (March 26, 2009, 6:38 a.m.)
Deposited	6 years, 8 months ago (Dec. 20, 2018, 4:27 p.m.)
Indexed	1 month, 2 weeks ago (July 14, 2025, 11:29 p.m.)
Issued	16 years, 5 months ago (April 1, 2009)
Published	16 years, 5 months ago (April 1, 2009)
Published Print	16 years, 5 months ago (April 1, 2009)

Funders 0

None

BibTeX

@article{Vajda_2009, title={Convergence and combination of methods in protein–protein docking}, volume={19}, ISSN={0959-440X}, url={http://dx.doi.org/10.1016/j.sbi.2009.02.008}, DOI={10.1016/j.sbi.2009.02.008}, number={2}, journal={Current Opinion in Structural Biology}, publisher={Elsevier BV}, author={Vajda, Sandor and Kozakov, Dima}, year={2009}, month=apr, pages={164–170} }

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