| [1] | Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S (2009) Biological process linkage networks. PLOS One 4: e5313. doi: 10.1371/journal.pone.0005313
|
| [2] | Gonzalez-Ruiz D, Gohlke H (2006) Targeting protein-protein interactions with small molecules: challenges and perspectives for computational binding epitope detection and ligand finding. Curr Med Chem 13: 2607–2625. doi: 10.2174/092986706778201530
|
| [3] | Metz A, Ciglia E, Gohlke H (2012) Modulating protein-protein interactions: from structural determinants of binding to druggability prediction to application. Curr Pharm Des 18: 4630–4647. doi: 10.2174/138161212802651553
|
| [4] | Brinda KV, Vishveshwara S (2005) Oligomeric protein structure networks: insights into protein-protein interactions. BMC Bioinformatics 6: 296. doi: 10.1186/1471-2105-6-296
|
| [5] | Ofran Y, Rost B (2007) Protein-protein interaction hotspots carved into sequences. PLOS Comput Biol 3: e119. doi: 10.1371/journal.pcbi.0030119
|
| [6] | Reichmann D, Rahat O, Cohen M, Neuvirth H, Schreiber G (2007) The molecular architecture of protein-protein binding sites. Curr Opin Struct Biol 17: 67–76. doi: 10.1016/j.sbi.2007.01.004
|
| [7] | Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280: 1–9. doi: 10.1006/jmbi.1998.1843
|
| [8] | Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267: 383–386. doi: 10.1126/science.7529940
|
| [9] | Metz A, Pfleger C, Kopitz H, Pfeiffer-Marek S, Baringhaus KH, et al. (2012) Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface. J Chem Inf Model 52: 120–133. doi: 10.1021/ci200322s
|
| [10] | Krüger DM, Gohlke H (2010) DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. Nucleic Acids Res 38: W480–486. doi: 10.1093/nar/gkq471
|
| [11] | Aloy P, Russell RB (2005) Structure-based systems biology: a zoom lens for the cell. FEBS Lett 579: 1854–1858. doi: 10.1016/j.febslet.2005.02.014
|
| [12] | Smith GR, Sternberg MJ (2002) Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 12: 28–35. doi: 10.1016/s0959-440x(02)00285-3
|
| [13] | Andrusier N, Mashiach E, Nussinov R, Wolfson HJ (2008) Principles of flexible protein-protein docking. Proteins 73: 271–289. doi: 10.1002/prot.22170
|
| [14] | Garzon JI, Lopez-Blanco JR, Pons C, Kovacs J, Abagyan R, et al. (2009) FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics 25: 2544–2551. doi: 10.1093/bioinformatics/btp447
|
| [15] | 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. J Mol Biol 331: 281–299. doi: 10.1016/s0022-2836(03)00670-3
|
| [16] | Vajda S, Kozakov D (2009) Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol 19: 164–170. doi: 10.1016/j.sbi.2009.02.008
|
| [17] | Ritchie DW (2008) Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 9: 1–15. doi: 10.2174/138920308783565741
|
| [18] | Bonvin AM (2006) Flexible protein-protein docking. Curr Opin Struct Biol 16: 194–200. doi: 10.1016/j.sbi.2006.02.002
|
| [19] | Basdevant N, Borgis D, Ha-Duong T (2007) A coarse-grained protein-protein potential derived from an all-atom force field. J Phys Chem B 111: 9390–9399. doi: 10.1021/jp0727190
|
| [20] | Fernandez-Recio J, Totrov M, Abagyan R (2003) ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 52: 113–117. doi: 10.1002/prot.10383
|
| [21] | Cheng TM, Blundell TL, Fernandez-Recio J (2007) pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 68: 503–515. doi: 10.1002/prot.21419
|
| [22] | Bertonati C, Honig B, Alexov E (2007) Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys J 92: 1891–1899. doi: 10.1529/biophysj.106.092122
|
| [23] | Vajda S, Sippl M, Novotny J (1997) Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol 7: 222–228. doi: 10.1016/s0959-440x(97)80029-2
|
| [24] | Pierce B, Weng Z (2007) ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 67: 1078–1086. doi: 10.1002/prot.21373
|
| [25] | Andrusier N, Nussinov R, Wolfson HJ (2007) FireDock: fast interaction refinement in molecular docking. Proteins 69: 139–159. doi: 10.1002/prot.21495
|
| [26] | Sippl MJ (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213: 859–883. doi: 10.1016/s0022-2836(05)80269-4
|
| [27] | Moont G, Gabb HA, Sternberg MJ (1999) Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 35: 364–373. doi: 10.1002/(sici)1097-0134(19990515)35:3<364::aid-prot11>3.3.co;2-w
|
| [28] | Glaser F, Steinberg DM, Vakser IA, Ben-Tal N (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 43: 89–102. doi: 10.1002/1097-0134(20010501)43:2<89::aid-prot1021>3.0.co;2-h
|
| [29] | Huang SY, Zou X (2008) An iterative knowledge-based scoring function for protein-protein recognition. Proteins 72: 557–579. doi: 10.1002/prot.21949
|
| [30] | Liu S, Vakser IA (2011) DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. BMC Bioinformatics 12: 280. doi: 10.1186/1471-2105-12-280
|
| [31] | Rajgaria R, McAllister SR, Floudas CA (2006) A novel high resolution Calpha–Calpha distance dependent force field based on a high quality decoy set. Proteins 65: 726–741. doi: 10.1002/prot.21149
|
| [32] | Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, et al. (2007) Integrating statistical pair potentials into protein complex prediction. Proteins 69: 511–520. doi: 10.1002/prot.21502
|
| [33] | Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S (2008) DARS (Decoys As the Reference State) potentials for protein-protein docking. Biophys J 95: 4217–4227. doi: 10.1529/biophysj.108.135814
|
| [34] | Lyskov S, Gray JJ (2008) The RosettaDock server for local protein-protein docking. Nucleic Acids Res 36: W233–238. doi: 10.1093/nar/gkn216
|
| [35] | Zacharias M (2003) Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 12: 1271–1282. doi: 10.1110/ps.0239303
|
| [36] | Tovchigrechko A, Vakser IA (2005) Development and testing of an automated approach to protein docking. Proteins 60: 296–301. doi: 10.1002/prot.20573
|
| [37] | Sippl MJ (1995) Knowledge-based potentials for proteins. Curr Opin Struct Biol 5: 229–235. doi: 10.1016/0959-440x(95)80081-6
|
| [38] | Gohlke H, Hendlich M, Klebe G (2000) Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 295: 337–356. doi: 10.1006/jmbi.1999.3371
|
| [39] | Pfeffer P, Gohlke H (2007) DrugScoreRNA–knowledge-based scoring function to predict RNA-ligand interactions. J Chem Inf Model 47: 1868–1876. doi: 10.1021/ci700134p
|
| [40] | Zhang C, Liu S, Zhu Q, Zhou Y (2005) A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J Med Chem 48: 2325–2335. doi: 10.1021/jm049314d
|
| [41] | Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL 3rd (2004) Assessing scoring functions for protein-ligand interactions. J Med Chem 47: 3032–3047. doi: 10.1021/jm030489h
|
| [42] | Tobi D (2010) Designing coarse grained-and atom based-potentials for protein-protein docking. BMC Struct Biol 10: 40. doi: 10.1186/1472-6807-10-40
|
| [43] | Kozakov D, Brenke R, Comeau SR, Vajda S (2006) PIPER: an FFT-based protein docking program with pairwise potentials. Proteins 65: 392–406. doi: 10.1002/prot.21117
|
| [44] | Viswanath S, Ravikant DV, Elber R (2013) Improving ranking of models for protein complexes with side chain modeling and atomic potentials. Proteins 81: 592–606. doi: 10.1002/prot.24214
|
| [45] | Kazemi S, Kruger DM, Sirockin F, Gohlke H (2009) Elastic potential grids: accurate and efficient representation of intermolecular interactions for fully flexible docking. ChemMedChem 4: 1264–1268. doi: 10.1002/cmdc.200900146
|
| [46] | Krüger DM, Jessen G, Gohlke H (2012) How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces? J Chem Inf Model 52: 2807–2811. doi: 10.1021/ci3003599
|
| [47] | Gohlke H, Klebe G (2002) DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. J Med Chem 45: 4153–4170. doi: 10.1021/jm020808p
|
| [48] | Krüger DM, Bergs J, Kazemi S, Gohlke H (2011) Target Flexibility in RNA？Ligand Docking Modeled by Elastic Potential Grids. ACS Med Chem Lett 2: 489–493. doi: 10.1021/ml100217h
|
| [49] | Kurcinski M, Kolinski A (2007) Hierarchical modeling of protein interactions. J Mol Model 13: 691–698. doi: 10.1007/s00894-007-0177-8
|
| [50] | Li YC, Zeng ZH (2008) Empirical parameters for estimating protein-protein binding energies: number of short- and long-distance atom-atom contacts. Protein Pept Lett 15: 223–231. doi: 10.2174/092986608783489634
|
| [51] | Hwang H, Pierce B, Mintseris J, Janin J, Weng Z (2008) Protein-protein docking benchmark version 3.0. Proteins 73: 705–709. doi: 10.1002/prot.22106
|
| [52] | Case TAD, Cheatham TE III, Simmerling CL, Wang J, Duke RE, et al.. (2012) AMBER 12. San Francisco.: University of California.
|
| [53] | Mendez R, Leplae R, De Maria L, Wodak SJ (2003) Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 52: 51–67. doi: 10.1002/prot.10393
|
| [54] | Cole JC, Taylor R, Verdonk ML (1998) Directional Preferences of Intermolecular Contacts to Hydrophobic Groups. Acta Cryst Sect D 54: 1183–1193. doi: 10.1107/s0907444998008932
|
| [55] | Maestro (2009) Maestro. version 9.1 ed. New York, NY: Schr？dinger, LLC.
|
| [56] | Xu D, Tsai CJ, Nussinov R (1997) Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Eng 10: 999–1012. doi: 10.1093/protein/10.9.999
|
| [57] | Tobi D, Bahar I (2006) Optimal design of protein docking potentials: efficiency and limitations. Proteins 62: 970–981. doi: 10.1002/prot.20859
|
| [58] | Tsai CJ, Kumar S, Ma B, Nussinov R (1999) Folding funnels, binding funnels, and protein function. Protein Sci 8: 1181–1190. doi: 10.1110/ps.8.6.1181
|
| [59] | Wang J, Verkhivker GM (2003) Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding. Phys Rev Lett 90: 188101. doi: 10.1103/physrevlett.90.188101
|
| [60] | Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, et al. (2002) Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective. Curr Opin Struct Biol 12: 197–203. doi: 10.1016/s0959-440x(02)00310-x
|
| [61] | Wang R, Lu Y, Wang S (2003) Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 46: 2287–2303. doi: 10.1021/jm0203783
|
| [62] | Mian IS, Bradwell AR, Olson AJ (1991) Structure, function and properties of antibody binding sites. J Mol Biol 217: 133–151. doi: 10.1016/0022-2836(91)90617-f
|
| [63] | Jackson RM (1999) Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: implications for the protein docking problem. Protein Sci 8: 603–613. doi: 10.1110/ps.8.3.603
|
| [64] | Sundberg EJ, Mariuzza RA (2002) Molecular recognition in antibody-antigen complexes. Adv Protein Chem 61: 119–160. doi: 10.1016/s0065-3233(02)61004-6
|
| [65] | Ramaraj T, Angel T, Dratz EA, Jesaitis AJ, Mumey B (2012) Antigen-antibody interface properties: Composition, residue interactions, and features of 53 non-redundant structures. Biochim Biophys Acta 1824: 520–532. doi: 10.1016/j.bbapap.2011.12.007
|
| [66] | Danley DE (2006) Crystallization to obtain protein-ligand complexes for structure-aided drug design. Acta Crystallogr D Biol Crystallogr 62: 569–575. doi: 10.1107/s0907444906012601
|
| [67] | Hinsen K (2008) Structural flexibility in proteins: impact of the crystal environment. Bioinformatics 24: 521–528. doi: 10.1093/bioinformatics/btm625
|
| [68] | Kramer B, Rarey M, Lengauer T (1999) Evaluation of the FlexX Incremental Construction Algorithm for Protein-Ligand Docking. Proteins 37: 145–156. doi: 10.1002/(sici)1097-0134(19991101)37:2<228::aid-prot8>3.0.co;2-8
|
| [69] | Radaev S, Zou Z, Huang T, Lafer EM, Hinck AP, et al. (2010) Ternary complex of transforming growth factor-beta1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily. J Biol Chem 285: 14806–14814. doi: 10.1074/jbc.m109.079921
|
| [70] | Tarricone C, Xiao B, Justin N, Walker PA, Rittinger K, et al. (2001) The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways. Nature 411: 215–219. doi: 10.1038/35075620
|
| [71] | Gamble TR, Vajdos FF, Yoo S, Worthylake DK, Houseweart M, et al. (1996) Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid. Cell 87: 1285–1294. doi: 10.1016/s0092-8674(00)81823-1
|
| [72] | Janin J, Rodier F (1995) Protein-protein interaction at crystal contacts. Proteins 23: 580–587. doi: 10.1002/prot.340230413
|
| [73] | Bahadur RP, Chakrabarti P, Rodier F, Janin J (2004) A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 336: 943–955. doi: 10.1016/j.jmb.2003.12.073
|
| [74] | Nissink JW, Murray C, Hartshorn M, Verdonk ML, Cole JC, et al. (2002) A new test set for validating predictions of protein-ligand interaction. Proteins 49: 457–471. doi: 10.1002/prot.10232
|
| [75] | Smith GR, Sternberg MJ, Bates PA (2005) The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol 347: 1077–1101. doi: 10.1016/j.jmb.2005.01.058
|
| [76] | Rajamani D, Thiel S, Vajda S, Camacho CJ (2004) Anchor residues in protein-protein interactions. Proc Natl Acad Sci U S A 101: 11287–11292. doi: 10.1073/pnas.0401942101
|
| [77] | Camacho CJ (2005) Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins 60: 245–251. doi: 10.1002/prot.20565
|
| [78] | Betts MJ, Sternberg MJ (1999) An analysis of conformational changes on protein-protein association: implications for predictive docking. Protein Eng 12: 271–283. doi: 10.1093/protein/12.4.271
|
| [79] | Goh CS, Milburn D, Gerstein M (2004) Conformational changes associated with protein-protein interactions. Curr Opin Struct Biol 14: 104–109. doi: 10.1016/j.sbi.2004.01.005
|
| [80] | Marsh JA, Teichmann SA, Forman-Kay JD (2012) Probing the diverse landscape of protein flexibility and binding. Curr Opin Struct Biol 22: 643–650. doi: 10.1016/j.sbi.2012.08.008
|
| [81] | Zacharias M (2010) Scoring and refinement of predicted protein-protein complexes. In: Zacharias M, editor. Protein-protein complexes: Analysis, modeling, and drug design. London: Imperial College Press. 236–271.
|
| [82] | Fernandez-Recio J, Totrov M, Abagyan R (2002) Soft protein-protein docking in internal coordinates. Protein Sci 11: 280–291. doi: 10.1110/ps.19202
|
| [83] | Ubbink M (2009) The courtship of proteins: understanding the encounter complex. FEBS Lett 583: 1060–1066. doi: 10.1016/j.febslet.2009.02.046
|
| [84] | Fawzi NL, Doucleff M, Suh JY, Clore GM (2010) Mechanistic details of a protein-protein association pathway revealed by paramagnetic relaxation enhancement titration measurements. Proc Natl Acad Sci U S A 107: 1379–1384. doi: 10.1073/pnas.0909370107
|
| [85] | Pierce B, Weng Z (2008) A combination of rescoring and refinement significantly improves protein docking performance. Proteins 72: 270–279. doi: 10.1002/prot.21920
|
| [86] | Lalonde S, Ehrhardt DW, Loque D, Chen J, Rhee SY, et al. (2008) Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations. Plant J 53: 610–635. doi: 10.1111/j.1365-313x.2007.03332.x
|
| [87] | Pazos F, Helmer-Citterich M, Ausiello G, Valencia A (1997) Correlated mutations contain information about protein-protein interaction. J Mol Biol 271: 511–523. doi: 10.1006/jmbi.1997.1198
|
| [88] | Cavasotto CN, Kovacs JA, Abagyan RA (2005) Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 127: 9632–9640. doi: 10.1021/ja042260c
|
| [89] | Mustard D, Ritchie DW (2005) Docking essential dynamics eigenstructures. Proteins 60: 269–274. doi: 10.1002/prot.20569
|
| [90] | Smith GR, Fitzjohn PW, Page CS, Bates PA (2005) Incorporation of flexibility into rigid-body docking: applications in rounds 3–5 of CAPRI. Proteins 60: 263–268. doi: 10.1002/prot.20568
|
| [91] | Otomo T, Tomchick DR, Otomo C, Panchal SC, Machius M, et al. (2005) Structural basis of actin filament nucleation and processive capping by a formin homology 2 domain. Nature 433: 488–494. doi: 10.1038/nature03251
|
| [92] | Marsh JA, Teichmann SA (2011) Relative solvent accessible surface area predicts protein conformational changes upon binding. Structure 19: 859–867. doi: 10.1016/j.str.2011.03.010
|
| [93] | Moal IH, Moretti R, Baker D, Fernandez-Recio J (2013) Scoring functions for protein-protein interactions. Curr Opin Struct Biol. 23: 862–867. doi: 10.1016/j.sbi.2013.06.017
|
