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For: Vanhee P, Stricher F, Baeten L, Verschueren E, Lenaerts T, Serrano L, Rousseau F, Schymkowitz J. Protein-Peptide Interactions Adopt the Same Structural Motifs as Monomeric Protein Folds. Structure 2009;17:1128-36. [DOI: 10.1016/j.str.2009.06.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 06/15/2009] [Accepted: 06/16/2009] [Indexed: 01/24/2023]
Number Cited by Other Article(s)
1
Hainzl T, Scortti M, Lindgren C, Grundström C, Krypotou E, Vázquez-Boland JA, Sauer-Eriksson AE. Structural basis of promiscuous inhibition of Listeria virulence activator PrfA by oligopeptides. Cell Rep 2025;44:115290. [PMID: 39970044 DOI: 10.1016/j.celrep.2025.115290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 11/20/2024] [Accepted: 01/17/2025] [Indexed: 02/21/2025]  Open
2
He J, Zou LN, Pareek V, Benkovic SJ. Multiplex mapping of protein-protein interaction interfaces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.28.635392. [PMID: 39975334 PMCID: PMC11838385 DOI: 10.1101/2025.01.28.635392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
3
Meador K, Castells-Graells R, Aguirre R, Sawaya MR, Arbing MA, Sherman T, Senarathne C, Yeates TO. A suite of designed protein cages using machine learning and protein fragment-based protocols. Structure 2024;32:751-765.e11. [PMID: 38513658 PMCID: PMC11162342 DOI: 10.1016/j.str.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/22/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
4
Meador K, Castells-Graells R, Aguirre R, Sawaya MR, Arbing MA, Sherman T, Senarathne C, Yeates TO. A Suite of Designed Protein Cages Using Machine Learning Algorithms and Protein Fragment-Based Protocols. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561468. [PMID: 37873110 PMCID: PMC10592684 DOI: 10.1101/2023.10.09.561468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
5
Chenna A, Khan WH, Dash R, Saraswat S, Chugh A, Rathore AS, Goel G. An efficient computational protocol for template-based design of peptides that inhibit interactions involving SARS-CoV-2 proteins. Proteins 2023;91:1222-1234. [PMID: 37283297 DOI: 10.1002/prot.26511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 06/08/2023]
6
Rui H, Ashton KS, Min J, Wang C, Potts PR. Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction. RSC Chem Biol 2023;4:192-215. [PMID: 36908699 PMCID: PMC9994104 DOI: 10.1039/d2cb00207h] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023]  Open
7
Zlobin A, Golovin A. Between Protein Fold and Nucleophile Identity: Multiscale Modeling of the TEV Protease Enzyme-Substrate Complex. ACS OMEGA 2022;7:40279-40292. [PMID: 36385818 PMCID: PMC9647873 DOI: 10.1021/acsomega.2c05201] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
8
Hurwitz N, Zaidman D, Wolfson HJ. Pep–Whisperer: Inhibitory peptide design. Proteins 2022;90:1886-1895. [DOI: 10.1002/prot.26384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 11/07/2022]
9
Swanson S, Sivaraman V, Grigoryan G, Keating AE. Tertiary motifs as building blocks for the design of protein-binding peptides. Protein Sci 2022;31:e4322. [PMID: 35634780 PMCID: PMC9088223 DOI: 10.1002/pro.4322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/07/2022]
10
Matching protein surface structural patches for high-resolution blind peptide docking. Proc Natl Acad Sci U S A 2022;119:e2121153119. [PMID: 35482919 PMCID: PMC9170164 DOI: 10.1073/pnas.2121153119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
11
Tsaban T, Varga JK, Avraham O, Ben-Aharon Z, Khramushin A, Schueler-Furman O. Harnessing protein folding neural networks for peptide-protein docking. Nat Commun 2022;13:176. [PMID: 35013344 PMCID: PMC8748686 DOI: 10.1038/s41467-021-27838-9] [Citation(s) in RCA: 301] [Impact Index Per Article: 100.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/10/2021] [Indexed: 12/31/2022]  Open
12
Xu X, Xiaoqin Zou. Predicting Protein-Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment. J Chem Inf Model 2022;62:27-39. [PMID: 34931833 PMCID: PMC9020583 DOI: 10.1021/acs.jcim.1c00836] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
13
Lu G, Li X, Zhang J, Xu Q. Molecular insight into the affinity, specificity and cross-reactivity of systematic hepatocellular carcinoma RALT interaction profile with human receptor tyrosine kinases. Amino Acids 2021;53:1715-1728. [PMID: 34618235 DOI: 10.1007/s00726-021-03083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/22/2021] [Indexed: 11/28/2022]
14
A novel peptide antagonist of the human growth hormone receptor. J Biol Chem 2021;296:100588. [PMID: 33774052 PMCID: PMC8086144 DOI: 10.1016/j.jbc.2021.100588] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/09/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022]  Open
15
Methods for Molecular Modelling of Protein Complexes. Methods Mol Biol 2021;2305:53-80. [PMID: 33950384 DOI: 10.1007/978-1-0716-1406-8_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
16
Bechor E, Zahavi A, Berdichevsky Y, Pick E. p67phox -derived self-assembled peptides prevent Nox2 NADPH oxidase activation by an auto-inhibitory mechanism. J Leukoc Biol 2020;109:657-673. [PMID: 32640488 DOI: 10.1002/jlb.4a0620-292r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/13/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022]  Open
17
Abbass J, Nebel JC. Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure. BMC Bioinformatics 2020;21:170. [PMID: 32357827 PMCID: PMC7195757 DOI: 10.1186/s12859-020-3491-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/13/2020] [Indexed: 11/10/2022]  Open
18
Mishra A, Bansal R, Sreenivasan S, Dash R, Joshi S, Singh R, Rathore AS, Goel G. Structure-Based Design of Small Peptide Ligands to Inhibit Early-Stage Protein Aggregation Nucleation. J Chem Inf Model 2020;60:3304-3314. [DOI: 10.1021/acs.jcim.0c00226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
19
Badaczewska-Dawid AE, Kolinski A, Kmiecik S. Computational reconstruction of atomistic protein structures from coarse-grained models. Comput Struct Biotechnol J 2019;18:162-176. [PMID: 31969975 PMCID: PMC6961067 DOI: 10.1016/j.csbj.2019.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 01/02/2023]  Open
20
Wen Z, He J, Tao H, Huang SY. PepBDB: a comprehensive structural database of biological peptide-protein interactions. Bioinformatics 2019;35:175-177. [PMID: 29982280 DOI: 10.1093/bioinformatics/bty579] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 07/04/2018] [Indexed: 02/01/2023]  Open
21
Saberi-Bosari S, Omary M, Lavoie A, Prodromou R, Day K, Menegatti S, San-Miguel A. Affordable Microfluidic Bead-Sorting Platform for Automated Selection of Porous Particles Functionalized with Bioactive Compounds. Sci Rep 2019;9:7210. [PMID: 31076584 PMCID: PMC6510793 DOI: 10.1038/s41598-019-42869-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 11/09/2022]  Open
22
Johansson-Åkhe I, Mirabello C, Wallner B. Predicting protein-peptide interaction sites using distant protein complexes as structural templates. Sci Rep 2019;9:4267. [PMID: 30862810 PMCID: PMC6414505 DOI: 10.1038/s41598-019-38498-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/31/2018] [Indexed: 01/07/2023]  Open
23
Litfin T, Yang Y, Zhou Y. SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. J Chem Inf Model 2019;59:924-930. [DOI: 10.1021/acs.jcim.8b00777] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
24
Xu X, Yan C, Zou X. MDockPeP: An ab-initio protein-peptide docking server. J Comput Chem 2018;39:2409-2413. [PMID: 30368849 DOI: 10.1002/jcc.25555] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/13/2018] [Accepted: 07/22/2018] [Indexed: 01/29/2023]
25
Farhadi T, Hashemian SM. Computer-aided design of amino acid-based therapeutics: a review. Drug Des Devel Ther 2018;12:1239-1254. [PMID: 29795978 PMCID: PMC5958949 DOI: 10.2147/dddt.s159767] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
26
Peptide Derivatives of Erythropoietin in the Treatment of Neuroinflammation and Neurodegeneration. THERAPEUTIC PROTEINS AND PEPTIDES 2018;112:309-357. [DOI: 10.1016/bs.apcsb.2018.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
27
Alam N, Goldstein O, Xia B, Porter KA, Kozakov D, Schueler-Furman O. High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. PLoS Comput Biol 2017;13:e1005905. [PMID: 29281622 PMCID: PMC5760072 DOI: 10.1371/journal.pcbi.1005905] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/09/2018] [Accepted: 11/29/2017] [Indexed: 11/24/2022]  Open
28
Bruzzoni-Giovanelli H, Alezra V, Wolff N, Dong CZ, Tuffery P, Rebollo A. Interfering peptides targeting protein-protein interactions: the next generation of drugs? Drug Discov Today 2017;23:272-285. [PMID: 29097277 DOI: 10.1016/j.drudis.2017.10.016] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/22/2017] [Accepted: 10/17/2017] [Indexed: 12/28/2022]
29
Mackenzie CO, Grigoryan G. Protein structural motifs in prediction and design. Curr Opin Struct Biol 2017;44:161-167. [PMID: 28460216 PMCID: PMC5513761 DOI: 10.1016/j.sbi.2017.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/18/2017] [Accepted: 03/28/2017] [Indexed: 01/11/2023]
30
Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Peptide-Protein Interactions. Methods Mol Biol 2017. [PMID: 28236233 DOI: 10.1007/978-1-4939-6798-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
31
Gomez-Gutierrez P, Campos PM, Vega M, Perez JJ. Identification of a Novel Inhibitory Allosteric Site in p38α. PLoS One 2016;11:e0167379. [PMID: 27898710 PMCID: PMC5127581 DOI: 10.1371/journal.pone.0167379] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 11/14/2016] [Indexed: 11/29/2022]  Open
32
Lima AH, dos Santos AM, Alves CN, Lameira J. Computed insight into a peptide inhibitor preventing the induced fit mechanism of MurA enzyme fromPseudomonas aeruginosa. Chem Biol Drug Des 2016;89:599-607. [DOI: 10.1111/cbdd.12882] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/16/2016] [Accepted: 09/29/2016] [Indexed: 11/28/2022]
33
Tertiary alphabet for the observable protein structural universe. Proc Natl Acad Sci U S A 2016;113:E7438-E7447. [PMID: 27810958 DOI: 10.1073/pnas.1607178113] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
34
Raghavender US. Analysis of residue conformations in peptides in Cambridge structural database and protein-peptide structural complexes. Chem Biol Drug Des 2016;89:428-442. [DOI: 10.1111/cbdd.12862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/27/2016] [Accepted: 08/25/2016] [Indexed: 01/29/2023]
35
Yan C, Xu X, Zou X. Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction. Structure 2016;24:1842-1853. [PMID: 27642160 DOI: 10.1016/j.str.2016.07.021] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/13/2016] [Accepted: 07/29/2016] [Indexed: 02/05/2023]
36
Obarska-Kosinska A, Iacoangeli A, Lepore R, Tramontano A. PepComposer: computational design of peptides binding to a given protein surface. Nucleic Acids Res 2016;44:W522-8. [PMID: 27131789 PMCID: PMC4987918 DOI: 10.1093/nar/gkw366] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/22/2016] [Indexed: 02/03/2023]  Open
37
Schindler CEM, de Vries SJ, Zacharias M. Fully Blind Peptide-Protein Docking with pepATTRACT. Structure 2015;23:1507-1515. [PMID: 26146186 DOI: 10.1016/j.str.2015.05.021] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/21/2015] [Accepted: 05/25/2015] [Indexed: 02/02/2023]
38
A Decoy Peptide that Disrupts TIRAP Recruitment to TLRs Is Protective in a Murine Model of Influenza. Cell Rep 2015;11:1941-52. [PMID: 26095366 DOI: 10.1016/j.celrep.2015.05.035] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 05/06/2015] [Accepted: 05/19/2015] [Indexed: 02/06/2023]  Open
39
Duffy FJ, O’Donovan D, Devocelle M, Moran N, O’Connell DJ, Shields DC. Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals Protein Interfaces Readily Targetable by Cyclic Peptides. J Chem Inf Model 2015;55:600-13. [DOI: 10.1021/ci500431q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
40
Yu H, Zhou P, Deng M, Shang Z. Indirect Readout in Protein-Peptide Recognition: A Different Story from Classical Biomolecular Recognition. J Chem Inf Model 2014;54:2022-32. [DOI: 10.1021/ci5000246] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
41
Téletchéa S, Stresing V, Hervouet S, Baud'huin M, Heymann MF, Bertho G, Charrier C, Ando K, Heymann D. Novel RANK antagonists for the treatment of bone-resorptive disease: theoretical predictions and experimental validation. J Bone Miner Res 2014;29:1466-77. [PMID: 24390798 DOI: 10.1002/jbmr.2170] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 12/17/2013] [Accepted: 01/01/2013] [Indexed: 12/15/2022]
42
Cukuroglu E, Gursoy A, Nussinov R, Keskin O. Non-redundant unique interface structures as templates for modeling protein interactions. PLoS One 2014;9:e86738. [PMID: 24475173 PMCID: PMC3903793 DOI: 10.1371/journal.pone.0086738] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 12/18/2013] [Indexed: 01/16/2023]  Open
43
Zhou Y, Ni Z, Chen K, Liu H, Chen L, Lian C, Yan L. Modeling Protein–Peptide Recognition Based on Classical Quantitative Structure–Affinity Relationship Approach: Implication for Proteome-Wide Inference of Peptide-Mediated Interactions. Protein J 2013;32:568-78. [DOI: 10.1007/s10930-013-9519-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
44
London N, Raveh B, Schueler-Furman O. Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how. Curr Opin Struct Biol 2013;23:894-902. [PMID: 24138780 DOI: 10.1016/j.sbi.2013.07.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 11/25/2022]
45
Chang TM, Cooper RJ, Williams ER. Locating protonated amines in clathrates. J Am Chem Soc 2013;135:14821-30. [PMID: 24007314 DOI: 10.1021/ja407414d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
46
Han KQ, Wu G, Lv F. Development of QSAR-Improved Statistical Potential for the Structure-Based Analysis of ProteinPeptide Binding Affinities. Mol Inform 2013;32:783-92. [DOI: 10.1002/minf.201300064] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 06/21/2013] [Indexed: 12/21/2022]
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Tian F, Tan R, Guo T, Zhou P, Yang L. Fast and reliable prediction of domain–peptide binding affinity using coarse-grained structure models. Biosystems 2013;113:40-9. [DOI: 10.1016/j.biosystems.2013.04.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 04/15/2013] [Accepted: 04/20/2013] [Indexed: 10/26/2022]
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Verschueren E, Vanhee P, Rousseau F, Schymkowitz J, Serrano L. Protein-peptide complex prediction through fragment interaction patterns. Structure 2013;21:789-97. [PMID: 23583037 DOI: 10.1016/j.str.2013.02.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 02/04/2013] [Accepted: 02/25/2013] [Indexed: 01/13/2023]
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Luo Q, Hamer R, Reinert G, Deane CM. Local network patterns in protein-protein interfaces. PLoS One 2013;8:e57031. [PMID: 23520460 PMCID: PMC3592891 DOI: 10.1371/journal.pone.0057031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 01/21/2013] [Indexed: 11/25/2022]  Open
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Zhang J, Grigoryan G. Mining tertiary structural motifs for assessment of designability. Methods Enzymol 2013;523:21-40. [PMID: 23422424 PMCID: PMC4222026 DOI: 10.1016/b978-0-12-394292-0.00002-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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