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For: Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali ŞK, Ozbek P, Ben Tal N, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Patapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol 2011;414:289-302. [PMID: 22001016 PMCID: PMC3839241 DOI: 10.1016/j.jmb.2011.09.031] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 09/08/2011] [Accepted: 09/16/2011] [Indexed: 11/26/2022]
Number Cited by Other Article(s)
1
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]
2
Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez‐Lumbreras LA, Fernandez‐Recio J, Harmalkar A, Chu L, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang S, Roel‐Touris J, Jimenez‐Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas‐Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman‐Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota‐Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda‐Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins 2023;91:1658-1683. [PMID: 37905971 PMCID: PMC10841881 DOI: 10.1002/prot.26609] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 11/02/2023]
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 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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
4
Wodak SJ, Vajda S, Lensink MF, Kozakov D, Bates PA. Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes. Annu Rev Biophys 2023;52:183-206. [PMID: 36626764 PMCID: PMC10885158 DOI: 10.1146/annurev-biophys-102622-084607] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
5
Ferraz MVF, Neto JCS, Lins RD, Teixeira ES. An artificial neural network model to predict structure-based protein-protein free energy of binding from Rosetta-calculated properties. Phys Chem Chem Phys 2023;25:7257-7267. [PMID: 36810523 DOI: 10.1039/d2cp05644e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
6
Tsuchiya Y, Yamamori Y, Tomii K. Protein-protein interaction prediction methods: from docking-based to AI-based approaches. Biophys Rev 2022;14:1341-1348. [PMID: 36570321 PMCID: PMC9759050 DOI: 10.1007/s12551-022-01032-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]  Open
7
Listov D, Lipsh‐Sokolik R, Rosset S, Yang C, Correia BE, Fleishman SJ. Assessing and enhancing foldability in designed proteins. Protein Sci 2022;31:e4400. [PMID: 36040259 PMCID: PMC9375437 DOI: 10.1002/pro.4400] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 11/11/2022]
8
Desantis F, Miotto M, Di Rienzo L, Milanetti E, Ruocco G. Spatial organization of hydrophobic and charged residues affects protein thermal stability and binding affinity. Sci Rep 2022;12:12087. [PMID: 35840609 PMCID: PMC9287411 DOI: 10.1038/s41598-022-16338-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/08/2022] [Indexed: 11/12/2022]  Open
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: 0.5] [Reference Citation Analysis] [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
Ghalandari B, Yu Y, Ghorbani F, Warden AR, Ahmad KZ, Sang X, Huang S, Zhang Y, Su W, Divsalar A, Ding X. Polydopamine nanospheres coated with bovine serum albumin permit enhanced cell differentiation: fundamental mechanism and practical application for protein coating formation. NANOSCALE 2021;13:20098-20110. [PMID: 34846416 DOI: 10.1039/d1nr07469e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
11
Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, Giełdoń A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Ślusarz R, Wesołowski PA, Zięba K, Del Carpio Muñoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Vargas Honorato R, Jandova Z, Jiménez-García B, Koukos PI, Van Keulen S, Van Noort CW, Réau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodríguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, Dapkūnas J, Olechnovič K, Venclovas Č, Duan R, Qiu L, Xu X, Zhang S, Zou X, Wodak SJ. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins 2021;89:1800-1823. [PMID: 34453465 PMCID: PMC8616814 DOI: 10.1002/prot.26222] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/24/2021] [Accepted: 08/05/2021] [Indexed: 12/19/2022]
12
Protein-Protein Docking: Past, Present, and Future. Protein J 2021;41:1-26. [PMID: 34787783 DOI: 10.1007/s10930-021-10031-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
13
Using diverse potentials and scoring functions for the development of improved machine-learned models for protein-ligand affinity and docking pose prediction. J Comput Aided Mol Des 2021;35:1095-1123. [PMID: 34708263 DOI: 10.1007/s10822-021-00423-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
14
Peleg Y, Vincentelli R, Collins BM, Chen KE, Livingstone EK, Weeratunga S, Leneva N, Guo Q, Remans K, Perez K, Bjerga GEK, Larsen Ø, Vaněk O, Skořepa O, Jacquemin S, Poterszman A, Kjær S, Christodoulou E, Albeck S, Dym O, Ainbinder E, Unger T, Schuetz A, Matthes S, Bader M, de Marco A, Storici P, Semrau MS, Stolt-Bergner P, Aigner C, Suppmann S, Goldenzweig A, Fleishman SJ. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. J Mol Biol 2021;433:166964. [PMID: 33781758 DOI: 10.1016/j.jmb.2021.166964] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
15
Lopez-Hernandez AE, Xie Y, Guo W, Li L. The Electrostatic Features of Dengue Virus Capsid Assembly. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
16
Residue-based pharmacophore approaches to study protein-protein interactions. Curr Opin Struct Biol 2021;67:205-211. [PMID: 33486430 DOI: 10.1016/j.sbi.2020.12.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/04/2020] [Accepted: 12/28/2020] [Indexed: 01/22/2023]
17
Park J, Gill KS, Aghajani AA, Heredia JD, Choi H, Oberstein A, Procko E. Engineered receptors for human cytomegalovirus that are orthogonal to normal human biology. PLoS Pathog 2020;16:e1008647. [PMID: 32559251 PMCID: PMC7329128 DOI: 10.1371/journal.ppat.1008647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/01/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022]  Open
18
Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets. Biochim Biophys Acta Gen Subj 2020;1864:129535. [DOI: 10.1016/j.bbagen.2020.129535] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 11/18/2022]
19
Generating quantitative binding landscapes through fractional binding selections combined with deep sequencing and data normalization. Nat Commun 2020;11:297. [PMID: 31941882 PMCID: PMC6962383 DOI: 10.1038/s41467-019-13895-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 11/28/2019] [Indexed: 11/09/2022]  Open
20
Lensink MF, Nadzirin N, Velankar S, Wodak SJ. Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition. Proteins 2020;88:916-938. [DOI: 10.1002/prot.25870] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/19/2019] [Accepted: 12/26/2019] [Indexed: 12/19/2022]
21
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Subraman SRMV, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, de Beauchêne IC, Maigret B, Devignes MD, Echartea MER, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Merideth BR, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins 2019;87:1200-1221. [PMID: 31612567 PMCID: PMC7274794 DOI: 10.1002/prot.25838] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/28/2022]
22
Treado JD, Mei Z, Regan L, O’Hern CS. Void distributions reveal structural link between jammed packings and protein cores. Phys Rev E 2019;99:022416. [PMID: 30934238 PMCID: PMC6902428 DOI: 10.1103/physreve.99.022416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Indexed: 11/07/2022]
23
León I, Alonso ER, Cabezas C, Mata S, Alonso JL. Unveiling the n→π* interactions in dipeptides. Commun Chem 2019. [DOI: 10.1038/s42004-018-0103-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
24
Sormanni P, Aprile FA, Vendruscolo M. Third generation antibody discovery methods: in silico rational design. Chem Soc Rev 2018;47:9137-9157. [PMID: 30298157 DOI: 10.1039/c8cs00523k] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
25
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: 6.2] [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
26
Raucci R, Laine E, Carbone A. Local Interaction Signal Analysis Predicts Protein-Protein Binding Affinity. Structure 2018;26:905-915.e4. [PMID: 29779789 DOI: 10.1016/j.str.2018.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/06/2018] [Accepted: 04/10/2018] [Indexed: 12/27/2022]
27
Gaines JC, Acebes S, Virrueta A, Butler M, Regan L, O'Hern CS. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. Proteins 2018;86:581-591. [PMID: 29427530 PMCID: PMC5912992 DOI: 10.1002/prot.25479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/23/2018] [Accepted: 02/06/2018] [Indexed: 12/26/2022]
28
Kuroda D, Tsumoto K. Antibody Affinity Maturation by Computational Design. Methods Mol Biol 2018;1827:15-34. [PMID: 30196490 DOI: 10.1007/978-1-4939-8648-4_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
29
Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ. The challenge of modeling protein assemblies: the CASP12-CAPRI experiment. Proteins 2017;86 Suppl 1:257-273. [PMID: 29127686 DOI: 10.1002/prot.25419] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/31/2017] [Accepted: 11/07/2017] [Indexed: 12/18/2022]
30
Tramontano A. The computational prediction of protein assemblies. Curr Opin Struct Biol 2017;46:170-175. [PMID: 29102305 DOI: 10.1016/j.sbi.2017.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
31
Structure-based cross-docking analysis of antibody-antigen interactions. Sci Rep 2017;7:8145. [PMID: 28811664 PMCID: PMC5557897 DOI: 10.1038/s41598-017-08414-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/10/2017] [Indexed: 12/02/2022]  Open
32
Marcu O, Dodson EJ, Alam N, Sperber M, Kozakov D, Lensink MF, Schueler-Furman O. FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility. Proteins 2017;85:445-462. [PMID: 28002624 PMCID: PMC6618814 DOI: 10.1002/prot.25230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/15/2016] [Accepted: 11/23/2016] [Indexed: 12/21/2022]
33
Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning. Proc Natl Acad Sci U S A 2017;114:2265-2270. [PMID: 28196882 DOI: 10.1073/pnas.1614437114] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
34
Wei Q, La D, Kihara D. BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns. Methods Mol Biol 2017;1529:279-289. [PMID: 27914057 DOI: 10.1007/978-1-4939-6637-0_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches. Methods Mol Biol 2016. [PMID: 27924488 DOI: 10.1007/978-1-4939-6563-2_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
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Yap EH, Fiser A. ProtLID, a Residue-Based Pharmacophore Approach to Identify Cognate Protein Ligands in the Immunoglobulin Superfamily. Structure 2016;24:2217-2226. [PMID: 27889206 PMCID: PMC5444293 DOI: 10.1016/j.str.2016.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 07/26/2016] [Accepted: 10/25/2016] [Indexed: 10/20/2022]
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Lensink MF, Velankar S, Wodak SJ. Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition. Proteins 2016;85:359-377. [PMID: 27865038 DOI: 10.1002/prot.25215] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 12/19/2022]
38
Riley TP, Ayres CM, Hellman LM, Singh NK, Cosiano M, Cimons JM, Anderson MJ, Piepenbrink KH, Pierce BG, Weng Z, Baker BM. A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Eng Des Sel 2016;29:595-606. [PMID: 27624308 PMCID: PMC5181382 DOI: 10.1093/protein/gzw050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 11/13/2022]  Open
39
Laine E, Carbone A. Protein social behavior makes a stronger signal for partner identification than surface geometry. Proteins 2016;85:137-154. [PMID: 27802579 PMCID: PMC5242317 DOI: 10.1002/prot.25206] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/10/2016] [Accepted: 10/20/2016] [Indexed: 01/26/2023]
40
Dygut J, Kalinowska B, Banach M, Piwowar M, Konieczny L, Roterman I. Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes. Int J Mol Sci 2016;17:ijms17101741. [PMID: 27763556 PMCID: PMC5085769 DOI: 10.3390/ijms17101741] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/30/2016] [Accepted: 10/11/2016] [Indexed: 12/20/2022]  Open
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Harris DT, Wang N, Riley TP, Anderson SD, Singh NK, Procko E, Baker BM, Kranz DM. Deep Mutational Scans as a Guide to Engineering High Affinity T Cell Receptor Interactions with Peptide-bound Major Histocompatibility Complex. J Biol Chem 2016;291:24566-24578. [PMID: 27681597 DOI: 10.1074/jbc.m116.748681] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/15/2016] [Indexed: 11/06/2022]  Open
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Shimba N, Kamiya N, Nakamura H. Model Building of Antibody–Antigen Complex Structures Using GBSA Scores. J Chem Inf Model 2016;56:2005-2012. [DOI: 10.1021/acs.jcim.6b00066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
43
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RAG, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JPGLM, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond ASJ, Visscher K, Kastritis PL, Bonvin AMJJ, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins 2016;84 Suppl 1:323-48. [PMID: 27122118 PMCID: PMC5030136 DOI: 10.1002/prot.25007] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 12/30/2015] [Accepted: 02/02/2016] [Indexed: 12/26/2022]
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Bale JB, Gonen S, Liu Y, Sheffler W, Ellis D, Thomas C, Cascio D, Yeates TO, Gonen T, King NP, Baker D. Accurate design of megadalton-scale two-component icosahedral protein complexes. Science 2016;353:389-94. [PMID: 27463675 PMCID: PMC5485857 DOI: 10.1126/science.aaf8818] [Citation(s) in RCA: 388] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/21/2016] [Indexed: 12/24/2022]
45
Regan L, Caballero D, Hinrichsen MR, Virrueta A, Williams DM, O'Hern CS. Protein design: Past, present, and future. Biopolymers 2016;104:334-50. [PMID: 25784145 DOI: 10.1002/bip.22639] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/05/2015] [Accepted: 03/07/2015] [Indexed: 01/16/2023]
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de Ruyck J, Brysbaert G, Blossey R, Lensink MF. Molecular docking as a popular tool in drug design, an in silico travel. Adv Appl Bioinform Chem 2016;9:1-11. [PMID: 27390530 PMCID: PMC4930227 DOI: 10.2147/aabc.s105289] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016;1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
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Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol 2016;12:e1004619. [PMID: 27124275 PMCID: PMC4849799 DOI: 10.1371/journal.pcbi.1004619] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
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Hoque MT, Yang Y, Mishra A, Zhou Y. s DFIRE : Sequence‐specific statistical energy function for protein structure prediction by decoy selections. J Comput Chem 2016;37:1119-24. [DOI: 10.1002/jcc.24298] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 12/06/2015] [Accepted: 12/13/2015] [Indexed: 12/15/2022]
50
Sirin S, Apgar JR, Bennett EM, Keating AE. AB-Bind: Antibody binding mutational database for computational affinity predictions. Protein Sci 2016;25:393-409. [PMID: 26473627 PMCID: PMC4815335 DOI: 10.1002/pro.2829] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/09/2015] [Accepted: 10/12/2015] [Indexed: 12/26/2022]
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