Near-Native Selections from Docking Decoys 53. Tovchigrechko A, Vakser IA. Development and testing of an auto- mated approach to protein docking. Proteins 2005;60:296–301. 54. Zhang C, Liu S, Zhou Y. Docking prediction using biological infor- mation, ZDOCK sampling technique and clusterization guided by the DFIRE statistical energy function. Proteins 2005;60:314– 318. 55. Jackson RM, Gabb HA, Sternberg MJ. Rapid refinement of protein interfaces incorporating solvation: application to the docking prob- lem. J Mol Biol 1998;276:265–285. 56. Lorber DM, Udo MK, Shoichet BK. Protein–protein docking with multiple residue conformations and residue substitutions. Protein Sci. 2002;11:1393–1408. 57. Fernandez-Recio J, Totrov M, Abagyan R. Soft protein–protein docking in internal coordinates. Protein Sci 2002;11:280–291. 58. Wang C, Schueler-Furman O, Baker D. Improved side-chain mod- eling for protein–protein docking. Protein Sci 2005;14:1328– 1339. 59. Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 2003;53:693–707. 60. Kowalsman N, Eisenstein M. Inherent limitations in protein– protein docking procedures. Bioinformatics 2007;23:421–426. 61. Chen R, Mintseris J, Janin J, Weng Z. A protein–protein docking benchmark. Proteins 2003;52:88–91. 62. Liang S, Grishin N. Effective scoring function for protein sequence design. Proteins 2004;54:271–281. 63. Lazaridis T, Karplus M. Effective energy function for proteins in so- lution. Proteins 1999;35:133–152. 64. Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 2000;97:10383–10388. 65. Liang S, Grishin NV. Side-chain modelling with an optimized scor- ing functions. Protein Sci 2002;11:322–331. 66. Dunbrack RJ, Cohen F. Bayesian statistical analysis of protein side- chain rotamer preferences. Protein Sci 1997;6:1661–1681. 67. Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side- chain amide orientation. J Mol Biol 1999;285:1735–1747. 68. Zou X, Sun Y, Kuntz ID. Inclusion of solvation in ligand binding free energy calculations using the generalized-born model. J Am Chem Soc 1999;121:8033–8043. 69. Conte LL, Chothia C, Janin J. The atomic structure of protein– protein recognition sites. J Mol Biol 1999;285:2177–2198. 70. Brooijmans N, Sharp K, Kuntz I. Stability of macromolecular com- plexes. Proteins 2002;48:645–653. 71. Gray JJ, Moughan SE, Kortemme T, Schueler-Furman O, Misura KMS, Morozov AV, Baker D. Protein–protein docking predictions for the CAPRI experiment. Proteins 2003;52:118–122. DOI 10.1002/prot PROTEINS 253