Erratum: The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design (J. Chem. Theory Comput. (2017) 13: 6 (3031-3048) DOI: 10.1021/acs.jctc.7b00125);The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

Journal of Chemical Theory and Computation

Volumn 13, Issue 6, 2017, Pages 3031-3048

  Alford, Rebecca F ^a   Leaver Fay, Andrew ^b   Jeliazkov, Jeliazko R ^c   O'Meara, Matthew J ^d   DiMaio, Frank P ^e   Park, Hahnbeom ^f   Shapovalov, Maxim V ^g   Renfrew, P Douglas ^h,i   Mulligan, Vikram K ^f   Kappel, Kalli ^j   Labonte, Jason W ^a   Pacella, Michael S ^k   Bonneau, Richard ^h,i   Bradley, Philip ^l   Dunbrack, Roland L ^g   Das, Rhiju ^j   Baker, David ^f   Kuhlman, Brian ^b   Kortemme, Tanja ^d   Gray, Jeffrey J ^a,c  

^a Johns Hopkins University   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^c JOHNS HOPKINS UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^f UNIVERSITY OF WASHINGTON   (United States)

^g FOX CHASE CANCER CENTER   (United States)

^h NEW YORK UNIVERSITY   (United States)

ⁱ FLATIRON INSTITUTE   (United States)

^j STANFORD UNIVERSITY   (United States)

^k Johns Hopkins University   (United States)

^l USA   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE;

CHEMISTRY; GENETICS; MACROMOLECULE; METABOLISM; MOLECULAR DYNAMICS; MUTATION; PROTEIN CONFORMATION; STATIC ELECTRICITY; THERMODYNAMICS;

HIV PROTEASE; MACROMOLECULAR SUBSTANCES; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN CONFORMATION; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 85020732573     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.2c00500     Document Type: Erratum

References (121)

1. Kuhlman, B.; Baker, D. Native Protein Sequences Are close to Optimal for Their Structures Proc. Natl. Acad. Sci. U. S. A. 2000, 97 (19) 10383-10388 10.1073/pnas.97.19.10383
2. Richardson, J. S. The Anatomy and Taxonomy of Protein Structure Adv. Protein Chem. 1981, 34, 167-339 10.1016/S0065-3233(08)60520-3
3. Leaver-Fay, A.; Tyka, M.; Lewis, S. M.; Lange, O. F.; Thompson, J.; Jacak, R.; Kaufman, K. W.; Renfrew, P. D.; Smith, C. A.; Sheffler, W.; Davis, I. W.; Cooper, S.; Treuille, A.; Mandell, D. J.; Richter, F.; Ban, Y.-E. A.; Fleishman, S. J.; Corn, J. E.; Kim, D. E.; Lyskov, S.; Berrondo, M.; Mentzer, S.; Popović, Z.; Havranek, J. J.; Karanicolas, J.; Das, R.; Meiler, J.; Kortemme, T.; Gray, J. J.; Kuhlman, B.; Baker, D.; Bradley, P. Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules Methods Enzymol. 2011, 487, 545-574 10.1016/B978-0-12-381270-4.00019-6
4. Anfinsen, C. B. Principles That Govern the Folding of Protein Chains Science 1973, 181 (4096) 223-230 10.1126/science.181.4096.223
5. Jones, J. E. On the Determination of Molecular Fields.-I. From the Variation of the Viscosity of a Gas with Temperature Proc. R. Soc. London, Ser. A 1924, 106, 441-462 10.1098/rspa.1924.0081
6. Jones, J. E. On the Determination of Molecular Fields.-II. From the Equation of State of a Gas Proc. R. Soc. London, Ser. A 1924, 106, 463-477 10.1098/rspa.1924.0082
7. Levitt, M.; Lifson, S. Refinement of Protein Conformations Using a Macromolecular Energy Minimization Procedure J. Mol. Biol. 1969, 46 (2) 269-279 10.1016/0022-2836(69)90421-5
8. Urey, H. C.; Bradley, C. A. The Vibrations of Pentatonic Tetrahedral Molecules Phys. Rev. 1931, 38 (11) 1969-1978 10.1103/PhysRev.38.1969
9. Westheimer, F. Calculation of the Magnitude of Steric Effects. In Steric Effects in Organic Chemistry; Newman, M. S., Ed.; Wiley: New York, 1956; pp 523-555.
10. Lifson, S.; Warshel, A. Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and N-Alkane Molecules J. Chem. Phys. 1968, 49 (11) 5116-5129 10.1063/1.1670007
11. Warshel, A.; Lifson, S. Consistent Force Field Calculations. II. Crystal Structures, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations, and Enthalpies of Alkanes J. Chem. Phys. 1970, 53 (2) 582-594 10.1063/1.1674031
12. Levitt, M. Energy Refinement of Hen Egg-White Lysozyme J. Mol. Biol. 1974, 82 (3) 393-420 10.1016/0022-2836(74)90599-3
13. Gelin, B. R.; Karplus, M. Sidechain Torsional Potentials and Motion of Amino Acids in Porteins: Bovine Pancreatic Trypsin Inhibitor Proc. Natl. Acad. Sci. U. S. A. 1975, 72 (6) 2002-2006 10.1073/pnas.72.6.2002
14. Levinthal, C.; Wodak, S. J.; Kahn, P.; Dadivanian, A. K. Hemoglobin Interaction in Sickle Cell Fibers. I: Theoretical Approaches to the Molecular Contacts Proc. Natl. Acad. Sci. U. S. A. 1975, 72 (4) 1330-1334 10.1073/pnas.72.4.1330
15. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1996, 118 (9) 2309-2309 10.1021/ja955032e
16. Mayo, S. L.; Olafson, B. D.; Goddard, W. A. DREIDING: A Generic Force Field for Molecular Simulations J. Phys. Chem. 1990, 94 (26) 8897-8909 10.1021/j100389a010
17. Jorgensen, W. L.; Tirado-Rives, J. The OPLS [Optimized Potentials for Liquid Simulations] Potential Functions for Proteins, Energy Minimizations for Crystals of Cyclic Peptides and Crambin J. Am. Chem. Soc. 1988, 110 (6) 1657-1666 10.1021/ja00214a001
18. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations J. Comput. Chem. 1983, 4 (2) 187-217 10.1002/jcc.540040211
19. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The Biomolecular Simulation Program J. Comput. Chem. 2009, 30 (10) 1545-1614 10.1002/jcc.21287
20. Sun, H. COMPASS: An Ab Initio Force-Field Optimized for Condensed-Phase Applications Overview with Details on Alkane and Benzene Compounds J. Phys. Chem. B 1998, 102 (38) 7338-7364 10.1021/jp980939v
21. Tanaka, S.; Scheraga, H. A. Model of Protein Folding: Inclusion of Short-, Medium-, and Long-Range Interactions Proc. Natl. Acad. Sci. U. S. A. 1975, 72 (10) 3802-3806 10.1073/pnas.72.10.3802
22. Tanaka, S.; Scheraga, H. A. Model of Protein Folding: Incorporation of a One-Dimensional Short-Range (Ising) Model into a Three-Dimensional Model Proc. Natl. Acad. Sci. U. S. A. 1977, 74 (4) 1320-1323 10.1073/pnas.74.4.1320
23. Miyazawa, S.; Jernigan, R. L. Residue-Residue Potentials with a Favorable Contact Pair Term and an Unfavorable High Packing Density Term, for Simulation and Threading J. Mol. Biol. 1996, 256 (3) 623-644 10.1006/jmbi.1996.0114
24. Wilmanns, M.; Eisenberg, D. Three-Dimensional Profiles from Residue-Pair Preferences: Identification of Sequences with Beta/alpha-Barrel Fold Proc. Natl. Acad. Sci. U. S. A. 1993, 90 (4) 1379-1383 10.1073/pnas.90.4.1379
25. Jones, D. T.; Taylor, W. R.; Thornton, J. M. A New Approach to Protein Fold Recognition Nature 1992, 358 (6381) 86-89 10.1038/358086a0
26. Bowie, J. U.; Lüthy, R.; Eisenberg, D. A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure Science 1991, 253 (5016) 164-170 10.1126/science.1853201
27. Sippl, M. J. 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. 1990, 213 (4) 859-883 10.1016/S0022-2836(05)80269-4
28. Skolnick, J.; Kolinski, A. Simulations of the Folding of a Globular Protein Science 1990, 250 (4984) 1121-1125 10.1126/science.250.4984.1121
29. Bashford, D.; Case, D. A. Generalized Born Models of Macromolecular Solvation Effects Annu. Rev. Phys. Chem. 2000, 51 (1) 129-152 10.1146/annurev.physchem.51.1.129
30. Warshel, A.; Kato, M.; Pisliakov, A. Polarizable Force Fields: History, Test Cases, and Prospects J. Chem. Theory Comput. 2007, 3 (6) 2034-2045 10.1021/ct700127w
31. Simons, K. T.; Kooperberg, C.; Huang, E.; Baker, D. Assembly of Protein Tertiary Structures from Fragments with Similar Local Sequences Using Simulated Annealing and Bayesian Scoring Functions J. Mol. Biol. 1997, 268 (1) 209-225 10.1006/jmbi.1997.0959
32. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28 (1) 235-242 10.1093/nar/28.1.235
33. Simons, K. T.; Ruczinski, I.; Kooperberg, C.; Fox, B. A.; Bystroff, C.; Baker, D. Improved Recognition of Native-like Protein Structures Using a Combination of Sequence-Dependent and Sequence-Independent Features of Proteins Proteins: Struct., Funct., Genet. 1999, 34 (1) 82-95 10.1002/(SICI)1097-0134(19990101)34:1<82::AID-PROT7>3.0.CO;2-A
34. Kuhlman, B.; Baker, D. Native Protein Sequences Are close to Optimal for Their Structures Proc. Natl. Acad. Sci. U. S. A. 2000, 97 (19) 10383-10388 10.1073/pnas.97.19.10383
35. Neria, E.; Fischer, S.; Karplus, M. Simulation of Activation Free Energies in Molecular Systems J. Chem. Phys. 1996, 105 (5) 1902-1921 10.1063/1.472061
36. Lazaridis, T.; Karplus, M. Effective Energy Function for Proteins in Solution Proteins: Struct., Funct., Genet. 1999, 35 (2) 133-152 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N
37. Dunbrack, R. L., Jr.; Cohen, F. E. Bayesian Statistical Analysis of Protein Side-Chain Rotamer Preferences Protein Sci. 1997, 6 (8) 1661-1681 10.1002/pro.5560060807
38. Kortemme, T.; Morozov, A. V.; Baker, D. An Orientation-Dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes J. Mol. Biol. 2003, 326 (4) 1239-1259 10.1016/S0022-2836(03)00021-4
39. Morozov, A. V.; Kortemme, T.; Tsemekhman, K.; Baker, D. Close Agreement between the Orientation Dependence of Hydrogen Bonds Observed in Protein Structures and Quantum Mechanical Calculations Proc. Natl. Acad. Sci. U. S. A. 2004, 101 (18) 6946-6951 10.1073/pnas.0307578101
40. Bradley, P.; Misura, K. M. S.; Baker, D. Toward High-Resolution de Novo Structure Prediction for Small Proteins Science 2005, 309 (5742) 1868-1871 10.1126/science.1113801
41. Kortemme, T.; Baker, D. A Simple Physical Model for Binding Energy Hot Spots in Protein-Protein Complexes Proc. Natl. Acad. Sci. U. S. A. 2002, 99 (22) 14116-14121 10.1073/pnas.202485799
42. Kortemme, T.; Kim, D. E.; Baker, D. Computational Alanine Scanning of Protein-Protein Interfaces Sci. STKE 2004, 2004 (219) pl2 10.1126/stke.2192004pl2
43. Gray, J. J.; Moughon, S.; Wang, C.; Schueler-Furman, O.; Kuhlman, B.; Rohl, C. A.; Baker, D. Protein-Protein Docking with Simultaneous Optimization of Rigid-Body Displacement and Side-Chain Conformations J. Mol. Biol. 2003, 331 (1) 281-299 10.1016/S0022-2836(03)00670-3
44. Meiler, J.; Baker, D. ROSETTALIGAND: Protein-Small Molecule Docking with Full Side-Chain Flexibility Proteins: Struct., Funct., Genet. 2006, 65 (3) 538-548 10.1002/prot.21086
45. Kortemme, T.; Joachimiak, L. A.; Bullock, A. N.; Schuler, A. D.; Stoddard, B. L.; Baker, D. Computational Redesign of Protein-Protein Interaction Specificity Nat. Struct. Mol. Biol. 2004, 11 (4) 371-379 10.1038/nsmb749
46. Kuhlman, B.; Dantas, G.; Ireton, G. C.; Varani, G.; Stoddard, B. L.; Baker, D. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy Science 2003, 302 (5649) 1364-1368 10.1126/science.1089427
47. Chevalier, B. S.; Kortemme, T.; Chadsey, M. S.; Baker, D.; Monnat, R. J.; Stoddard, B. L. Design, Activity, and Structure of a Highly Specific Artificial Endonuclease Mol. Cell 2002, 10 (4) 895-905 10.1016/S1097-2765(02)00690-1
48. Rohl, C. A.; Strauss, C. E. M.; Misura, K. M. S.; Baker, D. Protein Structure Prediction Using Rosetta Methods Enzymol. 2004, 383, 66-93 10.1016/S0076-6879(04)83004-0
49. O'Meara, M. J.; Leaver-Fay, A.; Tyka, M. D.; Stein, A.; Houlihan, K.; DiMaio, F.; Bradley, P.; Kortemme, T.; Baker, D.; Snoeyink, J.; Kuhlman, B. Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta J. Chem. Theory Comput. 2015, 11 (2) 609-622 10.1021/ct500864r
50. Park, H.; Bradley, P.; Greisen, P., Jr.; Liu, Y.; Mulligan, V. K.; Kim, D. E.; Baker, D.; DiMaio, F. Simultaneous Optimization of Biomolecular Energy Function on Features from Small Molecules and Macromolecules J. Chem. Theory Comput. 2016, 12 (12) 6201-6212 10.1021/acs.jctc.6b00819
51. Leaver-Fay, A.; O'Meara, M. J.; Tyka, M.; Jacak, R.; Song, Y.; Kellogg, E. H.; Thompson, J.; Davis, I. W.; Pache, R. A.; Lyskov, S.; Gray, J. J.; Kortemme, T.; Richardson, J. S.; Havranek, J. J.; Snoeyink, J.; Baker, D.; Kuhlman, B. Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement Methods Enzymol. 2013, 523, 109-143 10.1016/B978-0-12-394292-0.00006-0
52. Shapovalov, M. V.; Dunbrack, R. L. A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions Structure 2011, 19 (6) 844-858 10.1016/j.str.2011.03.019
53. DiMaio, F.; Song, Y.; Li, X.; Brunner, M. J.; Xu, C.; Conticello, V.; Egelman, E.; Marlovits, T. C.; Cheng, Y.; Baker, D. Atomic-Accuracy Models from 4.5-Å Cryo-Electron Microscopy Data with Density-Guided Iterative Local Refinement Nat. Methods 2015, 12 (4) 361-365 10.1038/nmeth.3286
54. Vortmeier, G.; DeLuca, S. H.; Els-Heindl, S.; Chollet, C.; Scheidt, H. A.; Beck-Sickinger, A. G.; Meiler, J.; Huster, D. Integrating Solid-State NMR and Computational Modeling to Investigate the Structure and Dynamics of Membrane-Associated Ghrelin PLoS One 2015, 10 (3) e0122444 10.1371/journal.pone.0122444
55. Correia, B. E.; Bates, J. T.; Loomis, R. J.; Baneyx, G.; Carrico, C.; Jardine, J. G.; Rupert, P.; Correnti, C.; Kalyuzhniy, O.; Vittal, V.; Connell, M. J.; Stevens, E.; Schroeter, A.; Chen, M.; Macpherson, S.; Serra, A. M.; Adachi, Y.; Holmes, M. A.; Li, Y.; Klevit, R. E.; Graham, B. S.; Wyatt, R. T.; Baker, D.; Strong, R. K.; Crowe, J. E.; Johnson, P. R.; Schief, W. R. Proof of Principle for Epitope-Focused Vaccine Design Nature 2014, 507 (7491) 201-206 10.1038/nature12966
56. Masica, D. L.; Schrier, S. B.; Specht, E. A.; Gray, J. J. De Novo Design of Peptide-Calcite Biomineralization Systems J. Am. Chem. Soc. 2010, 132 (35) 12252-12262 10.1021/ja1001086
57. King, N. P.; Bale, J. B.; Sheffler, W.; McNamara, D. E.; Gonen, S.; Gonen, T.; Yeates, T. O.; Baker, D. Accurate Design of Co-Assembling Multi-Component Protein Nanomaterials Nature 2014, 510 (7503) 103-108 10.1038/nature13404
58. Siegel, J. B.; Zanghellini, A.; Lovick, H. M.; Kiss, G.; Lambert, A. R.; St. Clair, J. L.; Gallaher, J. L.; Hilvert, D.; Gelb, M. H.; Stoddard, B. L.; Houk, K. N.; Michael, F. E.; Baker, D. Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction Science 2010, 329 (5989) 309-313 10.1126/science.1190239
59. Wolf, C.; Siegel, J. B.; Tinberg, C.; Camarca, A.; Gianfrani, C.; Paski, S.; Guan, R.; Montelione, G.; Baker, D.; Pultz, I. S. Engineering of Kuma030: A Gliadin Peptidase That Rapidly Degrades Immunogenic Gliadin Peptides in Gastric Conditions J. Am. Chem. Soc. 2015, 137 (40) 13106-13113 10.1021/jacs.5b08325
60. Kilambi, K. P.; Reddy, K.; Gray, J. J. Protein-Protein Docking with Dynamic Residue Protonation States PLoS Comput. Biol. 2014, 10 (12) e1004018 10.1371/journal.pcbi.1004018
61. Alford, R. F.; Koehler Leman, J.; Weitzner, B. D.; Duran, A. M.; Tilley, D. C.; Elazar, A.; Gray, J. J. An Integrated Framework Advancing Membrane Protein Modeling and Design PLoS Comput. Biol. 2015, 11 (9) e1004398 10.1371/journal.pcbi.1004398
62. Das, R.; Karanicolas, J.; Baker, D. Atomic Accuracy in Predicting and Designing Noncanonical RNA Structure Nat. Methods 2010, 7 (4) 291-294 10.1038/nmeth.1433
63. Thyme, S. B.; Baker, D.; Bradley, P. Improved Modeling of Side-Chain-Base Interactions and Plasticity in Protein-DNA Interface Design J. Mol. Biol. 2012, 419 (3-4) 255-274 10.1016/j.jmb.2012.03.005
64. Joyce, A. P.; Zhang, C.; Bradley, P.; Havranek, J. J. Structure-Based Modeling of Protein: DNA Specificity Briefings Funct. Genomics 2015, 14 (1) 39-49 10.1093/bfgp/elu044
65. Lemmon, G.; Meiler, J. Rosetta Ligand Docking with Flexible XML Protocols Methods Mol. Biol. 2012, 819, 143-155 10.1007/978-1-61779-465-0-10
66. Combs, S. A.; DeLuca, S. L.; DeLuca, S. H.; Lemmon, G. H.; Nannemann, D. P.; Nguyen, E. D.; Willis, J. R.; Sheehan, J. H.; Meiler, J. Small-Molecule Ligand Docking into Comparative Models with Rosetta Nat. Protoc. 2013, 8 (7) 1277-1298 10.1038/nprot.2013.074
67. Renfrew, P. D.; Choi, E. J.; Bonneau, R.; Kuhlman, B. Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design PLoS One 2012, 7 (3) e32637 10.1371/journal.pone.0032637
68. Drew, K.; Renfrew, P. D.; Craven, T. W.; Butterfoss, G. L.; Chou, F.-C.; Lyskov, S.; Bullock, B. N.; Watkins, A.; Labonte, J. W.; Pacella, M.; Kilambi, K. P.; Leaver-Fay, A.; Kuhlman, B.; Gray, J. J.; Bradley, P.; Kirshenbaum, K.; Arora, P. S.; Das, R.; Bonneau, R. Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design PLoS One 2013, 8 (7) e67051 10.1371/journal.pone.0067051
69. Bhardwaj, G.; Mulligan, V. K.; Bahl, C. D.; Gilmore, J. M.; Harvey, P. J.; Cheneval, O.; Buchko, G. W.; Pulavarti, S. V. S. R. K.; Kaas, Q.; Eletsky, A.; Huang, P.-S.; Johnsen, W. A.; Greisen, P. J.; Rocklin, G. J.; Song, Y.; Linsky, T. W.; Watkins, A.; Rettie, S. A.; Xu, X.; Carter, L. P.; Bonneau, R.; Olson, J. M.; Coutsias, E.; Correnti, C. E.; Szyperski, T.; Craik, D. J.; Baker, D. Accurate de Novo Design of Hyperstable Constrained Peptides Nature 2016, 538 (7625) 329-335 10.1038/nature19791
70. Labonte, J. W.; Adolf-Bryfogle, J.; Schief, W. R.; Gray, J. J. Residue-Centric Modeling and Design of Saccharide and Glycoconjugate Structures J. Comput. Chem. 2017, 38 (5) 276-287 10.1002/jcc.24679
71. Yanover, C.; Bradley, P. Extensive Protein and DNA Backbone Sampling Improves Structure-Based Specificity Prediction for C2H2 Zinc Fingers Nucleic Acids Res. 2011, 39 (11) 4564-4576 10.1093/nar/gkr048
72. Berkholz, D. S.; Driggers, C. M.; Shapovalov, M. V.; Dunbrack, R. L., Jr.; Karplus, P. A. Nonplanar Peptide Bonds in Proteins Are Common and Conserved but Not Biased toward Active Sites Proc. Natl. Acad. Sci. U. S. A. 2012, 109 (2) 449-453 10.1073/pnas.1107115108
73. Khatib, F.; Cooper, S.; Tyka, M. D.; Xu, K.; Makedon, I.; Popovic, Z.; Baker, D.; Players, F. Algorithm Discovery by Protein Folding Game Players Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (47) 18949-18953 10.1073/pnas.1115898108
74. Grigoryan, G.; Ochoa, A.; Keating, A. E. Computing van Der Waals Energies in the Context of the Rotamer Approximation Proteins: Struct., Funct., Genet. 2007, 68 (4) 863-878 10.1002/prot.21470
75. Dahiyat, B. I.; Mayo, S. L. Probing the Role of Packing Specificity in Protein Design Proc. Natl. Acad. Sci. U. S. A. 1997, 94 (19) 10172-10177 10.1073/pnas.94.19.10172
76. Warshel, A.; Russell, S. T. Calculations of Electrostatic Interactions in Biological Systems and in Solutions Q. Rev. Biophys. 1984, 17 (3) 283-422 10.1017/S0033583500005333
77. Hubbard, R. E.; Kamran Haider, M. Hydrogen Bonds in Proteins: Role and Strength. In Encyclopedia of Life Sciences; John Wiley & Sons: Chichester, U.K., 2010.
78. Li, X.-Z.; Walker, B.; Michaelides, A. Quantum Nature of the Hydrogen Bond Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (16) 6369-6373 10.1073/pnas.1016653108
79. Richardson, J. S.; Keedy, D. A.; Richardson, D. C. "The Plot" Thickens: More Data, More Dimensions, More Uses. In Biomolecular Forms and Functions: A Celebration of 50 Years of the Ramachandran Map; Bansal, M.; Srinivasan, N., Eds.; World Scientific: Singapore, 2013; pp 46-61.
80. Wang, C.; Bradley, P.; Baker, D. Protein-Protein Docking with Backbone Flexibility J. Mol. Biol. 2007, 373 (2) 503-519 10.1016/j.jmb.2007.07.050
81. Ho, B. K.; Thomas, A.; Brasseur, R. Revisiting the Ramachandran Plot: Hard-Sphere Repulsion, Electrostatics, and H-Bonding in the Alpha-Helix Protein Sci. 2003, 12 (11) 2508-2522 10.1110/ps.03235203
82. Wang, G.; Dunbrack, R. L. PISCES: A Protein Sequence Culling Server Bioinformatics 2003, 19 (12) 1589-1591 10.1093/bioinformatics/btg224
83. Ting, D.; Wang, G.; Shapovalov, M.; Mitra, R.; Jordan, M. I.; Dunbrack, R. L. Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model PLoS Comput. Biol. 2010, 6 (4) e1000763 10.1371/journal.pcbi.1000763
84. Finkelstein, A. V.; Badretdinov, A. Y.; Gutin, A. M. Why Do Protein Architectures Have Boltzmann-like Statistics? Proteins: Struct., Funct., Genet. 1995, 23 (2) 142-150 10.1002/prot.340230204
85. Shortle, D. Propensities, Probabilities, and the Boltzmann Hypothesis Protein Sci. 2003, 12 (6) 1298-1302 10.1110/ps.0306903
86. Lovell, S. C.; Word, J. M.; Richardson, J. S.; Richardson, D. C. The Penultimate Rotamer Library Proteins: Struct., Funct., Genet. 2000, 40 (3) 389-408 10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2
87. MacArthur, M. W.; Thornton, J. M. Influence of Proline Residues on Protein Conformation J. Mol. Biol. 1991, 218 (2) 397-412 10.1016/0022-2836(91)90721-H
88. McDonald, I. K.; Thornton, J. M. Satisfying Hydrogen Bonding Potential in Proteins J. Mol. Biol. 1994, 238 (5) 777-793 10.1006/jmbi.1994.1334
89. Conway, P.; Tyka, M. D.; DiMaio, F.; Konerding, D. E.; Baker, D. Relaxation of Backbone Bond Geometry Improves Protein Energy Landscape Modeling Protein Sci. 2014, 23 (1) 47-55 10.1002/pro.2389
90. Hall, M. B. Insight II, version 12000; Accelrys, Inc.: San Diego, CA, 2005.
91. Engh, R. A.; Huber, R. IUCr. Accurate Bond and Angle Parameters for X-Ray Protein Structure Refinement Acta Crystallogr., Sect. A: Found. Crystallogr. 1991, 47 (4) 392-400 10.1107/S0108767391001071
92. Renfrew, P. D.; Butterfoss, G. L.; Kuhlman, B. Using Quantum Mechanics to Improve Estimates of Amino Acid Side Chain Rotamer Energies Proteins: Struct., Funct., Genet. 2008, 71 (4) 1637-1646 10.1002/prot.21845
93. Barton, R. R.; Ivey, J. S. Nelder-Mead Simplex Modifications for Simulation Optimization Manage. Sci. 1996, 42 (7) 954-973 10.1287/mnsc.42.7.954
94. Ó Conchúir, S.; Barlow, K. A.; Pache, R. A.; Ollikainen, N.; Kundert, K.; O'Meara, M. J.; Smith, C. A.; Kortemme, T. A. Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design PLoS One 2015, 10 (9) e0130433 10.1371/journal.pone.0130433
95. Song, Y.; Tyka, M.; Leaver-Fay, A.; Thompson, J.; Baker, D. Structure-Guided Forcefield Optimization Proteins: Struct., Funct., Genet. 2011, 79 (6) 1898-1909 10.1002/prot.23013
96. Conway, P.; DiMaio, F. Improving Hybrid Statistical and Physical Forcefields through Local Structure Enumeration Protein Sci. 2016, 25 (8) 1525-1534 10.1002/pro.2956
97. Kellogg, E. H.; Leaver-Fay, A.; Baker, D. Role of Conformational Sampling in Computing Mutation-Induced Changes in Protein Structure and Stability Proteins: Struct., Funct., Genet. 2011, 79 (3) 830-838 10.1002/prot.22921
98. Mandell, D. J.; Coutsias, E. A.; Kortemme, T. Sub-Angstrom Accuracy in Protein Loop Reconstruction by Robotics-Inspired Conformational Sampling Nat. Methods 2009, 6 (8) 551-552 10.1038/nmeth0809-551
99. Tyka, M. D.; Keedy, D. A.; André, I.; DiMaio, F.; Song, Y.; Richardson, D. C.; Richardson, J. S.; Baker, D. Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping J. Mol. Biol. 2011, 405 (2) 607-618 10.1016/j.jmb.2010.11.008
100. Hwang, H.; Vreven, T.; Janin, J.; Weng, Z. Protein-Protein Docking Benchmark Version 4.0 Proteins: Struct., Funct., Genet. 2010, 78 (15) 3111-3114 10.1002/prot.22830
101. Chaudhury, S.; Berrondo, M.; Weitzner, B. D.; Muthu, P.; Bergman, H.; Gray, J. J. Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2 PLoS One 2011, 6 (8) e22477 10.1371/journal.pone.0022477
102. Raveh, B.; London, N.; Zimmerman, L.; Schueler-Furman, O. Rosetta FlexPepDock Ab-Initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors PLoS One 2011, 6 (4) e18934 10.1371/journal.pone.0018934
103. Song, Y.; DiMaio, F.; Wang, R. Y.-R.; Kim, D.; Miles, C.; Brunette, T.; Thompson, J.; Baker, D. High-Resolution Comparative Modeling with RosettaCM Structure 2013, 21 (10) 1735-1742 10.1016/j.str.2013.08.005
104. Altman, M. D.; Nalivaika, E. A.; Prabu-Jeyabalan, M.; Schiffer, C. A.; Tidor, B. Computational Design and Experimental Study of Tighter Binding Peptides to an Inactivated Mutant of HIV-1 Protease Proteins: Struct., Funct., Genet. 2008, 70 (3) 678-694 10.1002/prot.21514
105. Chaudhury, S.; Lyskov, S.; Gray, J. J. PyRosetta: A Script-Based Interface for Implementing Molecular Modeling Algorithms Using Rosetta Bioinformatics 2010, 26 (5) 689-691 10.1093/bioinformatics/btq007
106. Nybakken, G. E.; Oliphant, T.; Johnson, S.; Burke, S.; Diamond, M. S.; Fremont, D. H. Structural Basis of West Nile Virus Neutralization by a Therapeutic Antibody Nature 2005, 437 (7059) 764-769 10.1038/nature03956
107. Havranek, J. J.; Duarte, C. M.; Baker, D. A Simple Physical Model for the Prediction and Design of Protein-DNA Interactions J. Mol. Biol. 2004, 344 (1) 59-70 10.1016/j.jmb.2004.09.029
108. Chen, Y.; Kortemme, T.; Robertson, T.; Baker, D.; Varani, G. A New Hydrogen-Bonding Potential for the Design of Protein-RNA Interactions Predicts Specific Contacts and Discriminates Decoys Nucleic Acids Res. 2004, 32 (17) 5147-5162 10.1093/nar/gkh785
109. Renfrew, P. D.; Craven, T. W.; Butterfoss, G. L.; Kirshenbaum, K.; Bonneau, R. A Rotamer Library to Enable Modeling and Design of Peptoid Foldamers J. Am. Chem. Soc. 2014, 136 (24) 8772-8782 10.1021/ja503776z
110. Nivedha, A. K.; Thieker, D. F.; Makeneni, S.; Hu, H.; Woods, R. J. Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking J. Chem. Theory Comput. 2016, 12 (2) 892-901 10.1021/acs.jctc.5b00834
111. Nivedha, A. K.; Makeneni, S.; Foley, B. L.; Tessier, M. B.; Woods, R. J. Importance of Ligand Conformational Energies in Carbohydrate Docking: Sorting the Wheat from the Chaff J. Comput. Chem. 2014, 35 (7) 526-539 10.1002/jcc.23517
112. Das, R.; Baker, D. Automated de Novo Prediction of Native-like RNA Tertiary Structures Proc. Natl. Acad. Sci. U. S. A. 2007, 104 (37) 14664-14669 10.1073/pnas.0703836104
113. Sripakdeevong, P.; Kladwang, W.; Das, R. An Enumerative Stepwise Ansatz Enables Atomic-Accuracy RNA Loop Modeling Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (51) 20573-20578 10.1073/pnas.1106516108
114. Chou, F.-C.; Kladwang, W.; Kappel, K.; Das, R. Blind Tests of RNA Nearest-Neighbor Energy Prediction Proc. Natl. Acad. Sci. U. S. A. 2016, 113 (30) 8430-8435 10.1073/pnas.1523335113
115. Bazzoli, A.; Karanicolas, J. "Solvent Hydrogen-Bond Occlusion": A New Model of Polar Desolvation for Biomolecular Energetics J. Comput. Chem. 2017, 38, 1321-1331 10.1002/jcc.24740
116. Combs, S. A. Identification and Scoring of Partial Covalent Interactions in Proteins and Protein Ligand Complexes. Ph.D. Dissertation, Vanderbilt University, Nashville, TN, 2013.
117. Kilambi, K. P.; Gray, J. J. Rapid Calculation of Protein pKa Values Using Rosetta Biophys. J. 2012, 103 (3) 587-595 10.1016/j.bpj.2012.06.044
118. Barth, P.; Schonbrun, J.; Baker, D. Toward High-Resolution Prediction and Design of Transmembrane Helical Protein Structures Proc. Natl. Acad. Sci. U. S. A. 2007, 104 (40) 15682-15687 10.1073/pnas.0702515104
119. Yarov-Yarovoy, V.; Schonbrun, J.; Baker, D. Multipass Membrane Protein Structure Prediction Using Rosetta Proteins: Struct., Funct., Genet. 2006, 62 (4) 1010-1025 10.1002/prot.20817
120. Wang, Y.; Barth, P. Evolutionary-Guided de Novo Structure Prediction of Self-Associated Transmembrane Helical Proteins with near-Atomic Accuracy Nat. Commun. 2015, 6, 7196 10.1038/ncomms8196
121. Lazaridis, T. Effective Energy Function for Proteins in Lipid Membranes Proteins: Struct., Funct., Genet. 2003, 52 (2) 176-192 10.1002/prot.10410