| [1] | Garma L, Mukherjee S, Mitra P, Zhang Y (2012) How Many Protein-Protein Interactions Types Exist in Nature? PLoS ONE 7: e38913.
|
| [2] | Melquiond ASJ, Karaca E, Kastritis PL, Bonvin AMJJ (2011) Next challenges in protein-protein docking: from proteome to interactome and beyond. WIREs Comput Mol Sci 2: 642–651.
|
| [3] | Stein A, Mosca R, Aloy P (2011) Three-dimensional modeling of protein interactions and complexes is going “omics.”. Current Opinion in Structural Biology 21: 200–208.
|
| [4] | Nooren IMA, Thornton JM (2003) Diversity of protein–protein interactions. EMBO J 22: 3486–3492.
|
| [5] | Halperin I, Ma B, Wolfson H, Nussinov R (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins: Structure, Function, and Bioinformatics 47: 409–443.
|
| [6] | Stratmann D, Boelens R, Bonvin AMJJ (2011) Quantitative use of chemical shifts for the modeling of protein complexes. Proteins: Structure, Function, and Bioinformatics 79: 2662–2670.
|
| [7] | Cowieson NP, Kobe B, Martin JL (2008) United we stand: combining structural methods. Current Opinion in Structural Biology 18: 617–622.
|
| [8] | Karaca E, Bonvin AMJJ (2013) Advances in integrative modeling of biomolecular complexes. Methods 59: 372–381 doi:10.1016/j.ymeth.2012.12.004.
|
| [9] | Koehler J, Meiler J (2011) Expanding the utility of NMR restraints with paramagnetic compounds: background and practical aspects. Progress in Nuclear Magnetic Resonance Spectroscopy 59: 360–389.
|
| [10] | Schneider S, Zacharias M (2011) Scoring optimisation of unbound protein-protein docking including protein binding site predictions. J Mol Recognit 25: 15–23.
|
| [11] | Ritchie DW (2008) Recent progress and future directions in protein-protein docking. Current Protein and Peptide Science 9: 1–15.
|
| [12] | Moreira IS, Fernandes PA, Ramos MJ (2009) Protein-protein docking dealing with the unknown. J Comput Chem 31: 317–342.
|
| [13] | Smith GR, Sternberg MJE (2002) Prediction of protein–protein interactions by docking methods. Current Opinion in Structural Biology 12: 28–35.
|
| [14] | Vajda S, Kozakov D (2009) Convergence and combination of methods in protein–protein docking. Current Opinion in Structural Biology 19: 164–170.
|
| [15] | Sternberg MJ, Gabb HA, Jackson RM (1998) Predictive docking of protein-protein and protein-DNA complexes. Current Opinion in Structural Biology 8: 250–256.
|
| [16] | Lorenzen S, Zhang Y (2007) Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization. Protein Sci 16: 2716–2725.
|
| [17] | Zacharias M (2003) Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 12: 1271–1282.
|
| [18] | Chen R, Li L, Weng Z (2003) ZDOCK: An initial-stage protein-docking algorithm. Proteins: Structure, Function, and Bioinformatics 52: 80–87.
|
| [19] | Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, et al. (2003) Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations. Journal of Molecular Biology 331: 281–299.
|
| [20] | Dominguez C, Boelens R, Bonvin AMJJ (2003) HADDOCK: A Protein–Protein Docking Approach Based on Biochemical or Biophysical Information. J Am Chem Soc 125: 1731–1737.
|
| [21] | Fleishman SJ, Baker D (2012) Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution. Cell 149: 262–273.
|
| [22] | Fernández Recio J, Totrov M, Abagyan R (2003) ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins: Structure, Function, and Bioinformatics 52: 113–117.
|
| [23] | Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, et al. (2001) Protein docking using continuum electrostatics and geometric fit. Protein Engineering 14: 105–113.
|
| [24] | Aloy P, Querol E, Aviles FX, Sternberg MJE (2001) Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. Journal of Molecular Biology 311: 395–408.
|
| [25] | Tovchigrechko A, Vakser IA (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Research 34: W310–W314 doi:10.1093/nar/gkl206.
|
| [26] | Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) Geometry-based flexible and symmetric protein docking. Proteins: Structure, Function, and Bioinformatics 60: 224–231.
|
| [27] | Swendsen RH, Wang JS (1986) Replica Monte Carlo simulation of spin-glasses. Physical Review Letters 57: 2607–2609.
|
| [28] | Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chemical Physics Letters 314: 141–151.
|
| [29] | Kim YC, Tang C, Clore GM, Hummer G (2008) Replica exchange simulations of transient encounter complexes in protein–protein association. Proc Natl Acad Sci USA 105: 12855–12860.
|
| [30] | Lensink MF, Wodak SJ (2010) Docking and scoring protein interactions: CAPRI 2009. Proteins: Structure, Function, and Bioinformatics 78: 3073–3084 doi:10.1002/prot.22818.
|
| [31] | Chaudhury S, Berrondo M, Weitzner BD, Muthu P, Bergman H, et al. (2011) Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2. PLoS ONE 6: e22477.
|
| [32] | Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of State Calculations by Fast Computing Machines. J Chem Phys 21: 1087–1092.
|
| [33] | Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97–109.
|
| [34] | Gao Y, Douguet D, Tovchigrechko A, Vakser IA (2007) DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking. Proteins: Structure, Function, and Bioinformatics 69: 845–851.
|
| [35] | Fleishman SJ, Leaver-Fay A, Corn JE, Strauch E-M, Khare SD, et al. (2011) RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite. PLoS ONE 6: e20161.
|
| [36] | Méndez R, Leplae R, De Maria L, Wodak SJ (2003) Assessment of blind predictions of protein–protein interactions: current status of docking methods. Proteins: Structure, Function, and Bioinformatics 52: 51–67.
|
| [37] | Patriksson A, van der Spoel D (2008) A temperature predictor for parallel tempering simulations. Physical Chemistry Chemical Physics 10: 2073–2077.
|
| [38] | Rathore N, Chopra M, de Pablo JJ (2005) Optimal allocation of replicas in parallel tempering simulations. J Chem Phys 122: 024111 doi:10.1063/1.1831273.
|
| [39] | Sanbonmatsu KY, Garc a AE (2002) Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins: Structure, Function, and Bioinformatics 46: 225–234.
|
| [40] | Fukunishi H, Watanabe O, Takada S (2002) On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction. J Chem Phys 116: 9058 doi:10.1063/1.1472510.
|
| [41] | Hwang H, Vreven T, Pierce BG, Hung J-H, Weng Z (2010) Performance of ZDOCK and ZRANK in CAPRI rounds 13–19. Proteins: Structure, Function, and Bioinformatics 78: 3104–3110 doi:10.1002/prot.22764.
|
| [42] | Wiehe K, Pierce B, Tong WW, Hwang H, Mintseris J, et al. (2007) The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI. Proteins: Structure, Function, and Bioinformatics 69: 719–725.
|
| [43] | Wiehe K, Pierce B, Mintseris J, Tong WW, Anderson R, et al. (2005) ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins: Structure, Function, and Bioinformatics 60: 207–213 doi:10.1002/prot.20559.
|
| [44] | Lorenzen S, Zhang Y (2007) Identification of near-native structures by clustering protein docking conformations. Proteins: Structure, Function, and Bioinformatics 68: 187–194 doi:10.1002/prot.21442.
|
| [45] | Fraternali F, Cavallo L (2002) Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome. Nucleic Acids Research 30: 2950–2960.
|
| [46] | Kleinjung J, Fraternali F (2005) POPSCOMP: an automated interaction analysis of biomolecular complexes. Nucleic Acids Research 33: 342–346 doi:10.1093/nar/gki369.
|
| [47] | Tyka MD, Keedy DA, André I, DiMaio F, Song Y, et al. (2011) Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping. Journal of Molecular Biology 405: 607–618.
|
| [48] | Tyka MD, Jung K, Baker D (2012) Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. J Comput Chem 33: 2483–2491 doi:10.1002/jcc.23069.
|
