Protein-protein docking: overview and performance analysis.
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Zhiping Weng | Julian Mintseris | Kevin Wiehe | Brian Pierce | Matthew W. Peterson | Matthew W Peterson | Z. Weng | B. Pierce | J. Mintseris | K. Wiehe
[1] Sandor Vajda,et al. Classification of protein complexes based on docking difficulty , 2005, Proteins.
[2] Zhiping Weng,et al. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking , 2005, Bioinform..
[3] Li Li,et al. RDOCK: Refinement of rigid‐body protein docking predictions , 2003, Proteins.
[4] I. Vakser. Protein docking for low-resolution structures. , 1995, Protein engineering.
[5] Ilya A Vakser,et al. Development and testing of an automated approach to protein docking , 2005, Proteins.
[6] L. Krippahl,et al. BiGGER: A new (soft) docking algorithm for predicting protein interactions , 2000, Proteins.
[7] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[8] J M Blaney,et al. A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.
[9] Eleanor J. Gardiner,et al. Protein docking using a genetic algorithm , 2001, Proteins.
[10] L. T. Ten Eyck,et al. Protein docking using continuum electrostatics and geometric fit. , 2001, Protein engineering.
[11] Zhiping Weng,et al. A protein–protein docking benchmark , 2003, Proteins.
[12] R. Nussinov,et al. A geometry-based suite of molecular docking processes. , 1995, Journal of molecular biology.
[13] Z. Weng,et al. ZDOCK: An initial‐stage protein‐docking algorithm , 2003, Proteins.
[14] Z. Weng,et al. A novel shape complementarity scoring function for protein‐protein docking , 2003, Proteins.
[15] Z. Weng,et al. Optimizing protein representations with information theory. , 2004, Genome informatics. International Conference on Genome Informatics.
[16] R. Laskowski. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. , 1995, Journal of molecular graphics.
[17] Z. Weng,et al. Protein–protein docking benchmark 2.0: An update , 2005, Proteins.
[18] M. Sternberg,et al. An analysis of conformational changes on protein-protein association: implications for predictive docking. , 1999, Protein engineering.
[19] B. Rost,et al. Critical assessment of methods of protein structure prediction (CASP)—Round 6 , 2005 .
[20] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[21] Dima Kozakov,et al. Optimal clustering for detecting near-native conformations in protein docking. , 2005, Biophysical journal.
[22] Sandor Vajda,et al. ClusPro: an automated docking and discrimination method for the prediction of protein complexes , 2004, Bioinform..
[23] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..
[24] Sandor Vajda,et al. CAPRI: A Critical Assessment of PRedicted Interactions , 2003, Proteins.
[25] E. Katchalski‐Katzir,et al. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[26] C. DeLisi,et al. Determination of atomic desolvation energies from the structures of crystallized proteins. , 1997, Journal of molecular biology.
[27] Jeffrey J. Gray,et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. , 2003, Journal of molecular biology.
[28] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[29] W. Delano. The PyMOL Molecular Graphics System , 2002 .
[30] Roland L. Dunbrack,et al. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.
[31] Ruth Nussinov,et al. PatchDock and SymmDock: servers for rigid and symmetric docking , 2005, Nucleic Acids Res..
[32] M. Sternberg,et al. Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.
[33] C. Dominguez,et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.
[34] D. Ritchie,et al. Protein docking using spherical polar Fourier correlations , 2000, Proteins.
[35] Yuhua Duan,et al. Physicochemical and residue conservation calculations to improve the ranking of protein–protein docking solutions , 2005, Protein science : a publication of the Protein Society.
[36] Zhiping Weng,et al. Docking unbound proteins using shape complementarity, desolvation, and electrostatics , 2002, Proteins.
[37] Ruben Abagyan,et al. ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation , 1994, J. Comput. Chem..