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For: Shifman JM, Mayo SL. Exploring the origins of binding specificity through the computational redesign of calmodulin. Proc Natl Acad Sci U S A 2003;100:13274-9. [PMID: 14597710 PMCID: PMC263780 DOI: 10.1073/pnas.2234277100] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Bonadio A, Wenig BL, Hockla A, Radisky ES, Shifman JM. Designed Loop Extension Followed by Combinatorial Screening Confers High Specificity to a Broad Matrix MetalloproteinaseInhibitor. J Mol Biol 2023;435:168095. [PMID: 37068580 PMCID: PMC10312305 DOI: 10.1016/j.jmb.2023.168095] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 04/19/2023]
2
Bollella P, Edwardraja S, Guo Z, Vickers CE, Whitfield J, Walden P, Melman A, Alexandrov K, Katz E. Connecting Artificial Proteolytic and Electrochemical Signaling Systems with Caged Messenger Peptides. ACS Sens 2021;6:3596-3603. [PMID: 34637274 DOI: 10.1021/acssensors.1c00845] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
3
Nazet J, Lang E, Merkl R. Rosetta:MSF:NN: Boosting performance of multi-state computational protein design with a neural network. PLoS One 2021;16:e0256691. [PMID: 34437621 PMCID: PMC8389498 DOI: 10.1371/journal.pone.0256691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 08/12/2021] [Indexed: 12/05/2022]  Open
4
Sun B, Kekenes-Huskey PM. Assessing the Role of Calmodulin's Linker Flexibility in Target Binding. Int J Mol Sci 2021;22:ijms22094990. [PMID: 34066691 PMCID: PMC8125811 DOI: 10.3390/ijms22094990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022]  Open
5
Bissonnette S, Del Grosso E, Simon AJ, Plaxco KW, Ricci F, Vallée-Bélisle A. Optimizing the Specificity Window of Biomolecular Receptors Using Structure-Switching and Allostery. ACS Sens 2020;5:1937-1942. [PMID: 32297508 DOI: 10.1021/acssensors.0c00237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
6
Netzer R, Listov D, Lipsh R, Dym O, Albeck S, Knop O, Kleanthous C, Fleishman SJ. Ultrahigh specificity in a network of computationally designed protein-interaction pairs. Nat Commun 2018;9:5286. [PMID: 30538236 PMCID: PMC6290019 DOI: 10.1038/s41467-018-07722-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/21/2018] [Indexed: 01/21/2023]  Open
7
Shirian J, Arkadash V, Cohen I, Sapir T, Radisky ES, Papo N, Shifman JM. Converting a broad matrix metalloproteinase family inhibitor into a specific inhibitor of MMP-9 and MMP-14. FEBS Lett 2018;592:1122-1134. [PMID: 29473954 DOI: 10.1002/1873-3468.13016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/11/2018] [Accepted: 02/19/2018] [Indexed: 12/22/2022]
8
Chapman AM, McNaughton BR. Scratching the Surface: Resurfacing Proteins to Endow New Properties and Function. Cell Chem Biol 2017;23:543-553. [PMID: 27203375 DOI: 10.1016/j.chembiol.2016.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 12/22/2022]
9
Löffler P, Schmitz S, Hupfeld E, Sterner R, Merkl R. Rosetta:MSF: a modular framework for multi-state computational protein design. PLoS Comput Biol 2017;13:e1005600. [PMID: 28604768 PMCID: PMC5484525 DOI: 10.1371/journal.pcbi.1005600] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/26/2017] [Accepted: 05/27/2017] [Indexed: 12/20/2022]  Open
10
Hidden Markov model and Chapman Kolmogrov for protein structures prediction from images. Comput Biol Chem 2017;68:231-244. [DOI: 10.1016/j.compbiolchem.2017.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/11/2017] [Accepted: 04/11/2017] [Indexed: 11/20/2022]
11
Coluzza I. Computational protein design: a review. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017;29:143001. [PMID: 28140371 DOI: 10.1088/1361-648x/aa5c76] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
12
Achievements and Challenges in Computational Protein Design. Methods Mol Biol 2017;1529:21-94. [PMID: 27914045 DOI: 10.1007/978-1-4939-6637-0_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
13
Samish I. The Framework of Computational Protein Design. Methods Mol Biol 2017;1529:3-19. [PMID: 27914044 DOI: 10.1007/978-1-4939-6637-0_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
14
Brender JR, Shultis D, Khattak NA, Zhang Y. An Evolution-Based Approach to De Novo Protein Design. Methods Mol Biol 2017;1529:243-264. [PMID: 27914055 PMCID: PMC5667548 DOI: 10.1007/978-1-4939-6637-0_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
15
Rosenfeld L, Heyne M, Shifman JM, Papo N. Protein Engineering by Combined Computational and In Vitro Evolution Approaches. Trends Biochem Sci 2016;41:421-433. [PMID: 27061494 DOI: 10.1016/j.tibs.2016.03.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/29/2016] [Accepted: 03/09/2016] [Indexed: 12/30/2022]
16
Yan Z, Wang J. Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks. J Comput Aided Mol Des 2016;30:219-27. [DOI: 10.1007/s10822-016-9897-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/28/2016] [Indexed: 01/04/2023]
17
Kulkarni C, Lo M, Fraseur JG, Tirrell DA, Kinzer-Ursem TL. Bioorthogonal Chemoenzymatic Functionalization of Calmodulin for Bioconjugation Applications. Bioconjug Chem 2015;26:2153-60. [PMID: 26431265 DOI: 10.1021/acs.bioconjchem.5b00449] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
18
Tripathi S, Waxham MN, Cheung MS, Liu Y. Lessons in Protein Design from Combined Evolution and Conformational Dynamics. Sci Rep 2015;5:14259. [PMID: 26388515 PMCID: PMC4585694 DOI: 10.1038/srep14259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/21/2015] [Indexed: 11/09/2022]  Open
19
Computational design and experimental verification of a symmetric protein homodimer. Proc Natl Acad Sci U S A 2015;112:10714-9. [PMID: 26269568 DOI: 10.1073/pnas.1505072112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
20
Yan Z, Wang J. Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect. Proteins 2015;83:1632-42. [PMID: 26111900 DOI: 10.1002/prot.24848] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/03/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
21
Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Eur J Inorg Chem 2015;2015:3371-3390. [PMID: 27630532 PMCID: PMC5019575 DOI: 10.1002/ejic.201500470] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 12/26/2022]
22
Zheng F, Jewell H, Fitzpatrick J, Zhang J, Mierke DF, Grigoryan G. Computational design of selective peptides to discriminate between similar PDZ domains in an oncogenic pathway. J Mol Biol 2014;427:491-510. [PMID: 25451599 DOI: 10.1016/j.jmb.2014.10.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/21/2014] [Accepted: 10/23/2014] [Indexed: 11/25/2022]
23
Murciano-Calles J, McLaughlin ME, Erijman A, Hooda Y, Chakravorty N, Martinez JC, Shifman JM, Sidhu SS. Alteration of the C-Terminal Ligand Specificity of the Erbin PDZ Domain by Allosteric Mutational Effects. J Mol Biol 2014;426:3500-8. [DOI: 10.1016/j.jmb.2014.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 04/10/2014] [Accepted: 05/02/2014] [Indexed: 10/25/2022]
24
Lao BB, Drew K, Guarracino DA, Brewer TF, Heindel DW, Bonneau R, Arora PS. Rational design of topographical helix mimics as potent inhibitors of protein-protein interactions. J Am Chem Soc 2014;136:7877-88. [PMID: 24972345 PMCID: PMC4353027 DOI: 10.1021/ja502310r] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
25
Li M, Petukh M, Alexov E, Panchenko AR. Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity. J Chem Theory Comput 2014;10:1770-1780. [PMID: 24803870 PMCID: PMC3985714 DOI: 10.1021/ct401022c] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Indexed: 01/22/2023]
26
Davey JA, Chica RA. Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles. Proteins 2013;82:771-84. [DOI: 10.1002/prot.24457] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/07/2013] [Accepted: 10/21/2013] [Indexed: 11/11/2022]
27
Yan Z, Wang J. Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity. PLoS One 2013;8:e74443. [PMID: 24098651 PMCID: PMC3787031 DOI: 10.1371/journal.pone.0074443] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 08/02/2013] [Indexed: 12/14/2022]  Open
28
Mann JK, Wood JF, Stephan AF, Tzanakakis ES, Ferkey DM, Park S. Epitope-guided engineering of monobody binders for in vivo inhibition of Erk-2 signaling. ACS Chem Biol 2013;8:608-16. [PMID: 23227961 PMCID: PMC3600092 DOI: 10.1021/cb300579e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
29
Yan Z, Guo L, Hu L, Wang J. Specificity and affinity quantification of protein-protein interactions. Bioinformatics 2013;29:1127-33. [DOI: 10.1093/bioinformatics/btt121] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
30
Smith C, Shi C, Chroust M, Bliska T, Kelly M, Jacobson M, Kortemme T. Design of a Phosphorylatable PDZ Domain with Peptide-Specific Affinity Changes. Structure 2013;21:54-64. [DOI: 10.1016/j.str.2012.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/13/2012] [Accepted: 10/18/2012] [Indexed: 01/06/2023]
31
Computational Methods for Controlling Binding Specificity. Methods Enzymol 2013;523:41-59. [DOI: 10.1016/b978-0-12-394292-0.00003-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
32
Zuo Z, Gandhi NS, Arndt KM, Mancera RL. Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein. Biopolymers 2012;97:899-909. [DOI: 10.1002/bip.22099] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
33
Davey JA, Chica RA. Multistate approaches in computational protein design. Protein Sci 2012;21:1241-52. [PMID: 22811394 DOI: 10.1002/pro.2128] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/04/2012] [Accepted: 07/12/2012] [Indexed: 11/10/2022]
34
Sandhya S, Mudgal R, Jayadev C, Abhinandan KR, Sowdhamini R, Srinivasan N. Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins. MOLECULAR BIOSYSTEMS 2012;8:2076-84. [PMID: 22692068 DOI: 10.1039/c2mb25113b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
35
Alvizo O, Mittal S, Mayo SL, Schiffer CA. Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease. Protein Sci 2012;21:1029-41. [PMID: 22549928 DOI: 10.1002/pro.2086] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/23/2012] [Accepted: 04/10/2012] [Indexed: 02/02/2023]
36
Yu CM, Peng HP, Chen IC, Lee YC, Chen JB, Tsai KC, Chen CT, Chang JY, Yang EW, Hsu PC, Jian JW, Hsu HJ, Chang HJ, Hsu WL, Huang KF, Ma AC, Yang AS. Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface. PLoS One 2012;7:e33340. [PMID: 22457753 PMCID: PMC3310866 DOI: 10.1371/journal.pone.0033340] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 02/14/2012] [Indexed: 12/01/2022]  Open
37
Fleishman SJ, Khare SD, Koga N, Baker D. Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Sci 2011;20:753-7. [PMID: 21432939 DOI: 10.1002/pro.604] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
38
Lewis SM, Kuhlman BA. Anchored design of protein-protein interfaces. PLoS One 2011;6:e20872. [PMID: 21698112 PMCID: PMC3117852 DOI: 10.1371/journal.pone.0020872] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 05/11/2011] [Indexed: 12/26/2022]  Open
39
Polydorides S, Amara N, Aubard C, Plateau P, Simonson T, Archontis G. Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase. Proteins 2011;79:3448-68. [PMID: 21563215 DOI: 10.1002/prot.23042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 02/25/2011] [Accepted: 03/03/2011] [Indexed: 12/13/2022]
40
McQueen P, Donald LJ, Vo TN, Nguyen DH, Griffiths H, Shojania S, Standing KG, O'Neil JD. Tat peptide-calmodulin binding studies and bioinformatics of HIV-1 protein-calmodulin interactions. Proteins 2011;79:2233-46. [DOI: 10.1002/prot.23048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 03/18/2011] [Accepted: 03/22/2011] [Indexed: 01/08/2023]
41
Sharabi O, Yanover C, Dekel A, Shifman JM. Optimizing energy functions for protein-protein interface design. J Comput Chem 2011;32:23-32. [PMID: 20623647 DOI: 10.1002/jcc.21594] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
42
Sharabi O, Dekel A, Shifman JM. Triathlon for energy functions: who is the winner for design of protein-protein interactions? Proteins 2011;79:1487-98. [PMID: 21365678 DOI: 10.1002/prot.22977] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2010] [Revised: 12/19/2010] [Accepted: 12/22/2010] [Indexed: 11/09/2022]
43
Erijman A, Aizner Y, Shifman JM. Multispecific Recognition: Mechanism, Evolution, and Design. Biochemistry 2011;50:602-11. [DOI: 10.1021/bi101563v] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
44
van der Sloot AM, Quax WJ. Computational design of TNF ligand-based protein therapeutics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011;691:521-34. [PMID: 21153357 DOI: 10.1007/978-1-4419-6612-4_54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
45
Bhattacherjee A, Biswas P. Designing Misfolded Proteins by Energy Landscaping. J Phys Chem B 2010;115:113-9. [DOI: 10.1021/jp108416c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
46
Smith CA, Kortemme T. Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. J Mol Biol 2010;402:460-74. [PMID: 20654621 DOI: 10.1016/j.jmb.2010.07.032] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 07/07/2010] [Indexed: 11/27/2022]
47
Allen BD, Mayo SL. An efficient algorithm for multistate protein design based on FASTER. J Comput Chem 2010;31:904-16. [PMID: 19637210 DOI: 10.1002/jcc.21375] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
48
MacDonald JT, Maksimiak K, Sadowski MI, Taylor WR. De novo backbone scaffolds for protein design. Proteins 2010;78:1311-25. [PMID: 20017215 PMCID: PMC2841848 DOI: 10.1002/prot.22651] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
49
Filchtinski D, Sharabi O, Rüppel A, Vetter IR, Herrmann C, Shifman JM. What makes Ras an efficient molecular switch: a computational, biophysical, and structural study of Ras-GDP interactions with mutants of Raf. J Mol Biol 2010;399:422-35. [PMID: 20361980 DOI: 10.1016/j.jmb.2010.03.046] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2009] [Revised: 03/19/2010] [Accepted: 03/23/2010] [Indexed: 11/16/2022]
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Fromer M, Yanover C, Linial M. Design of multispecific protein sequences using probabilistic graphical modeling. Proteins 2010;78:530-47. [PMID: 19842166 DOI: 10.1002/prot.22575] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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