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For: Khafizov K, Madrid-Aliste C, Almo SC, Fiser A. Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative. Proc Natl Acad Sci U S A 2014;111:3733-8. [PMID: 24567391 DOI: 10.1073/pnas.1321614111] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [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
Hsu STD. Folding and functions of knotted proteins. Curr Opin Struct Biol 2023;83:102709. [PMID: 37778185 DOI: 10.1016/j.sbi.2023.102709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
2
Larrea-Sebal A, Jebari-Benslaiman S, Galicia-Garcia U, Jose-Urteaga AS, Uribe KB, Benito-Vicente A, Martín C. Predictive Modeling and Structure Analysis of Genetic Variants in Familial Hypercholesterolemia: Implications for Diagnosis and Protein Interaction Studies. Curr Atheroscler Rep 2023;25:839-859. [PMID: 37847331 PMCID: PMC10618353 DOI: 10.1007/s11883-023-01154-7] [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] [Accepted: 09/15/2023] [Indexed: 10/18/2023]
3
Pathira Kankanamge LS, Ruffner LA, Touch MM, Pina M, Beuning PJ, Ondrechen MJ. Functional annotation of haloacid dehalogenase superfamily structural genomics proteins. Biochem J 2023;480:1553-1569. [PMID: 37747786 DOI: 10.1042/bcj20230057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
4
AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms. Commun Biol 2023;6:160. [PMID: 36755055 PMCID: PMC9908985 DOI: 10.1038/s42003-023-04488-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023]  Open
5
Binder JL, Berendzen J, Stevens AO, He Y, Wang J, Dokholyan NV, Oprea TI. AlphaFold illuminates half of the dark human proteins. Curr Opin Struct Biol 2022;74:102372. [PMID: 35439658 PMCID: PMC10669925 DOI: 10.1016/j.sbi.2022.102372] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/02/2022] [Accepted: 03/13/2022] [Indexed: 01/05/2023]
6
Miñarro-Lleonar M, Ruiz-Carmona S, Alvarez-Garcia D, Schmidtke P, Barril X. Development of an Automatic Pipeline for Participation in the CELPP Challenge. Int J Mol Sci 2022;23:ijms23094756. [PMID: 35563148 PMCID: PMC9105952 DOI: 10.3390/ijms23094756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/01/2022]  Open
7
Adasme MF, Bolz SN, Al-Fatlawi A, Schroeder M. Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening. J Cheminform 2022;14:17. [PMID: 35292113 PMCID: PMC8922937 DOI: 10.1186/s13321-022-00592-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022]  Open
8
Mesdaghi S, Murphy DL, Sánchez Rodríguez F, Burgos-Mármol JJ, Rigden DJ. In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. F1000Res 2021;9:1395. [PMID: 33520197 PMCID: PMC7818093 DOI: 10.12688/f1000research.27676.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/11/2021] [Indexed: 01/07/2023]  Open
9
Mesdaghi S, Murphy DL, Sánchez Rodríguez F, Burgos-Mármol JJ, Rigden DJ. In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. F1000Res 2021;9:1395. [PMID: 33520197 PMCID: PMC7818093 DOI: 10.12688/f1000research.27676.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 01/07/2023]  Open
10
Zhang J, Ghadermarzi S, Kurgan L. Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes versus disordered proteins. Bioinformatics 2021;36:4729-4738. [PMID: 32860044 DOI: 10.1093/bioinformatics/btaa573] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/22/2020] [Accepted: 06/10/2020] [Indexed: 01/08/2023]  Open
11
NMR Structure Determinations of Small Proteins Using only One Fractionally 20% 13C- and Uniformly 100% 15N-Labeled Sample. Molecules 2021;26:molecules26030747. [PMID: 33535444 PMCID: PMC7867066 DOI: 10.3390/molecules26030747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/17/2022]  Open
12
Wilson IA, Stanfield RL. 50 Years of structural immunology. J Biol Chem 2021;296:100745. [PMID: 33957119 PMCID: PMC8163984 DOI: 10.1016/j.jbc.2021.100745] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]  Open
13
Golea-Secara A, Munteanu C, Sarbu M, Cretu OM, Velciov S, Vlad A, Bob F, Gadalean F, Gluhovschi C, Milas O, Simulescu A, Mogos-Stefan M, Patruica M, Petrica L, Zamfir AD. Urinary proteins detected using modern proteomics intervene in early type 2 diabetic kidney disease – a pilot study. Biomark Med 2020;14:1521-1536. [DOI: 10.2217/bmm-2020-0308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
14
Delhommel F, Gabel F, Sattler M. Current approaches for integrating solution NMR spectroscopy and small-angle scattering to study the structure and dynamics of biomolecular complexes. J Mol Biol 2020;432:2890-2912. [DOI: 10.1016/j.jmb.2020.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 01/24/2023]
15
Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies. J Comput Aided Mol Des 2019;33:887-903. [PMID: 31628659 DOI: 10.1007/s10822-019-00235-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/11/2019] [Indexed: 10/25/2022]
16
Mayol E, Campillo M, Cordomí A, Olivella M. Inter-residue interactions in alpha-helical transmembrane proteins. Bioinformatics 2019;35:2578-2584. [PMID: 30566615 DOI: 10.1093/bioinformatics/bty978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/19/2018] [Accepted: 12/17/2018] [Indexed: 01/23/2023]  Open
17
Negron C, Pearlman DA, del Angel G. Predicting mutations deleterious to function in beta-lactamase TEM1 using MM-GBSA. PLoS One 2019;14:e0214015. [PMID: 30889230 PMCID: PMC6424398 DOI: 10.1371/journal.pone.0214015] [Citation(s) in RCA: 11] [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: 11/28/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022]  Open
18
Braitbard M, Schneidman-Duhovny D, Kalisman N. Integrative Structure Modeling: Overview and Assessment. Annu Rev Biochem 2019;88:113-135. [PMID: 30830798 DOI: 10.1146/annurev-biochem-013118-111429] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
19
Viswanathan R, Fajardo E, Steinberg G, Haller M, Fiser A. Protein-protein binding supersites. PLoS Comput Biol 2019;15:e1006704. [PMID: 30615604 PMCID: PMC6336348 DOI: 10.1371/journal.pcbi.1006704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 01/17/2019] [Accepted: 12/05/2018] [Indexed: 11/19/2022]  Open
20
Trevizani R, Custódio FL. Supersecondary Structures and Fragment Libraries. Methods Mol Biol 2019;1958:283-295. [PMID: 30945224 DOI: 10.1007/978-1-4939-9161-7_14] [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] [Indexed: 06/09/2023]
21
Hu G, Wang K, Song J, Uversky VN, Kurgan L. Taxonomic Landscape of the Dark Proteomes: Whole-Proteome Scale Interplay Between Structural Darkness, Intrinsic Disorder, and Crystallization Propensity. Proteomics 2018;18:e1800243. [PMID: 30198635 DOI: 10.1002/pmic.201800243] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/30/2018] [Indexed: 12/14/2022]
22
Iyer MS, Joshi AG, Sowdhamini R. Genome-wide survey of remote homologues for protein domain superfamilies of known structure reveals unequal distribution across structural classes. Mol Omics 2018;14:266-280. [PMID: 29971307 DOI: 10.1039/c8mo00008e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
23
Unique function words characterize genomic proteins. Proc Natl Acad Sci U S A 2018;115:6703-6708. [PMID: 29895692 PMCID: PMC6042118 DOI: 10.1073/pnas.1801182115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
24
Validation of LDLr Activity as a Tool to Improve Genetic Diagnosis of Familial Hypercholesterolemia: A Retrospective on Functional Characterization of LDLr Variants. Int J Mol Sci 2018;19:ijms19061676. [PMID: 29874871 PMCID: PMC6032215 DOI: 10.3390/ijms19061676] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/28/2018] [Accepted: 06/04/2018] [Indexed: 12/11/2022]  Open
25
Ahmad S, Baseer S, Navid A, Ahmad F, Azam SS. An integrated computational hierarchy for identification of potent inhibitors against Shikimate Kinase enzyme from Shigella sonnei , a major cause of global dysentery. GENE REPORTS 2018;11:283-293. [DOI: 10.1016/j.genrep.2018.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
26
Xia Y, Fischer AW, Teixeira P, Weiner B, Meiler J. Integrated Structural Biology for α-Helical Membrane Protein Structure Determination. Structure 2018;26:657-666.e2. [PMID: 29526436 PMCID: PMC5884713 DOI: 10.1016/j.str.2018.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 06/14/2017] [Accepted: 02/05/2018] [Indexed: 01/12/2023]
27
Using molecular simulation to explore the nanoscale dynamics of the plant kinome. Biochem J 2018. [DOI: 10.1042/bcj20170299] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
28
Fowler PW, Cole K, Gordon NC, Kearns AM, Llewelyn MJ, Peto TEA, Crook DW, Walker AS. Robust Prediction of Resistance to Trimethoprim in Staphylococcus aureus. Cell Chem Biol 2018;25:339-349.e4. [PMID: 29307840 DOI: 10.1016/j.chembiol.2017.12.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/24/2017] [Accepted: 12/08/2017] [Indexed: 01/28/2023]
29
Meng F, Wang C, Kurgan L. fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization. BMC Bioinformatics 2018;18:580. [PMID: 29295714 PMCID: PMC6389161 DOI: 10.1186/s12859-017-1995-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/06/2017] [Indexed: 02/26/2023]  Open
30
Dey S, Levy ED. Inferring and Using Protein Quaternary Structure Information from Crystallographic Data. Methods Mol Biol 2018;1764:357-375. [PMID: 29605927 DOI: 10.1007/978-1-4939-7759-8_23] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
31
Zhang J, Ma Z, Kurgan L. Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains. Brief Bioinform 2017;20:1250-1268. [DOI: 10.1093/bib/bbx168] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/15/2017] [Indexed: 11/13/2022]  Open
32
Shamsi Z, Moffett AS, Shukla D. Enhanced unbiased sampling of protein dynamics using evolutionary coupling information. Sci Rep 2017;7:12700. [PMID: 28983093 PMCID: PMC5629199 DOI: 10.1038/s41598-017-12874-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 09/14/2017] [Indexed: 12/25/2022]  Open
33
Monzon AM, Zea DJ, Marino-Buslje C, Parisi G. Homology modeling in a dynamical world. Protein Sci 2017;26:2195-2206. [PMID: 28815769 DOI: 10.1002/pro.3274] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 12/31/2022]
34
Barril X. Computer-aided drug design: time to play with novel chemical matter. Expert Opin Drug Discov 2017;12:977-980. [PMID: 28756685 DOI: 10.1080/17460441.2017.1362386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
35
Inhester T, Bietz S, Hilbig M, Schmidt R, Rarey M. Index-Based Searching of Interaction Patterns in Large Collections of Protein–Ligand Interfaces. J Chem Inf Model 2017;57:148-158. [DOI: 10.1021/acs.jcim.6b00561] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
36
Dybas JM, Fiser A. Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds. Proteins 2016;84:1859-1874. [PMID: 27671894 PMCID: PMC5118133 DOI: 10.1002/prot.25169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 08/17/2016] [Accepted: 08/25/2016] [Indexed: 11/09/2022]
37
Identification of potent inhibitors for chromodomain-helicase- DNA-binding protein 1-like through moleculardocking studies. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1712-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
38
Gao Y, Hao W, Gu J, Liu D, Fan C, Chen Z, Deng L. PredPhos: an ensemble framework for structure-based prediction of phosphorylation sites. ACTA ACUST UNITED AC 2016;23:12. [PMID: 27437197 PMCID: PMC4943517 DOI: 10.1186/s40709-016-0042-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
39
Serrano P, Dutta SK, Proudfoot A, Mohanty B, Susac L, Martin B, Geralt M, Jaroszewski L, Godzik A, Elsliger M, Wilson IA, Wüthrich K. NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia. FEBS J 2016;283:3870-3881. [PMID: 27154589 DOI: 10.1111/febs.13751] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/12/2016] [Accepted: 05/04/2016] [Indexed: 12/12/2022]
40
Hong S, Kim D. Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds. Bioinformatics 2016;32:1709-15. [DOI: 10.1093/bioinformatics/btw032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/18/2016] [Indexed: 11/14/2022]  Open
41
Lobb B, Doxey AC. Novel function discovery through sequence and structural data mining. Curr Opin Struct Biol 2016;38:53-61. [DOI: 10.1016/j.sbi.2016.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/17/2016] [Accepted: 05/24/2016] [Indexed: 01/30/2023]
42
Margelevičius M. Bayesian nonparametrics in protein remote homology search. Bioinformatics 2016;32:2744-52. [DOI: 10.1093/bioinformatics/btw213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/14/2016] [Indexed: 11/14/2022]  Open
43
The impact of structural genomics: the first quindecennial. ACTA ACUST UNITED AC 2016;17:1-16. [PMID: 26935210 DOI: 10.1007/s10969-016-9201-5] [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] [Received: 12/12/2015] [Accepted: 02/17/2016] [Indexed: 12/21/2022]
44
Sfriso P, Duran-Frigola M, Mosca R, Emperador A, Aloy P, Orozco M. Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins. Structure 2016;24:116-126. [DOI: 10.1016/j.str.2015.10.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/13/2015] [Accepted: 10/17/2015] [Indexed: 12/12/2022]
45
Fusco D, Charbonneau P. Soft matter perspective on protein crystal assembly. Colloids Surf B Biointerfaces 2016;137:22-31. [DOI: 10.1016/j.colsurfb.2015.07.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/24/2023]
46
Unexpected features of the dark proteome. Proc Natl Acad Sci U S A 2015;112:15898-903. [PMID: 26578815 DOI: 10.1073/pnas.1508380112] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
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An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life. Sci Rep 2015;5:14717. [PMID: 26434770 PMCID: PMC4592975 DOI: 10.1038/srep14717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/07/2015] [Indexed: 11/14/2022]  Open
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AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators. J Mol Biol 2015;428:671-678. [PMID: 26410588 DOI: 10.1016/j.jmb.2015.09.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/04/2015] [Accepted: 09/17/2015] [Indexed: 11/20/2022]
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Computational approaches to study the effects of small genomic variations. J Mol Model 2015;21:251. [PMID: 26350246 DOI: 10.1007/s00894-015-2794-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/23/2015] [Indexed: 10/23/2022]
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Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W. X-ray crystallography over the past decade for novel drug discovery - where are we heading next? Expert Opin Drug Discov 2015;10:975-89. [PMID: 26177814 DOI: 10.1517/17460441.2015.1061991] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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