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For: Capra JA, Singh M. Characterization and prediction of residues determining protein functional specificity. ACTA ACUST UNITED AC 2008;24:1473-80. [PMID: 18450811 PMCID: PMC2718669 DOI: 10.1093/bioinformatics/btn214] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Number Cited by Other Article(s)
1
Cheng C, McCauley BS, Matulionis N, Vogelauer M, Camacho D, Christofk HR, Dang W, Irwin NAT, Kurdistani SK. Histone H3 cysteine 110 enhances iron metabolism and modulates replicative life span in Saccharomyces cerevisiae. SCIENCE ADVANCES 2025;11:eadv4082. [PMID: 40215312 PMCID: PMC11988410 DOI: 10.1126/sciadv.adv4082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 03/06/2025] [Indexed: 04/14/2025]
2
Yin J, Waman VP, Sen N, Firdaus-Raih M, Lam SD, Orengo C. Understanding the structural and functional diversity of ATP-PPases using protein domains and functional families in the CATH database. Structure 2025;33:613-631.e6. [PMID: 39826548 DOI: 10.1016/j.str.2024.12.016] [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: 10/31/2023] [Revised: 04/18/2024] [Accepted: 12/19/2024] [Indexed: 01/22/2025]
3
Hernández Berthet AS, Aptekmann AA, Tejero J, Sánchez IE, Noguera ME, Roman EA. Associating protein sequence positions with the modulation of quantitative phenotypes. Arch Biochem Biophys 2024;755:109979. [PMID: 38583654 DOI: 10.1016/j.abb.2024.109979] [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: 12/13/2023] [Revised: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
4
McWhite CD, Armour-Garb I, Singh M. Leveraging protein language models for accurate multiple sequence alignments. Genome Res 2023;33:1145-1153. [PMID: 37414576 PMCID: PMC10538487 DOI: 10.1101/gr.277675.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
5
Adeyelu T, Bordin N, Waman VP, Sadlej M, Sillitoe I, Moya-Garcia AA, Orengo CA. KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units. Biomolecules 2023;13:277. [PMID: 36830646 PMCID: PMC9953599 DOI: 10.3390/biom13020277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]  Open
6
Timonina DS, Suplatov DA. Analysis of Multiple Protein Alignments Using 3D-Structural Information on the Orientation of Amino Acid Side-Chains. Mol Biol 2022. [DOI: 10.1134/s0026893322040136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
7
McGreig JE, Uri H, Antczak M, Sternberg MJE, Michaelis M, Wass MN. 3DLigandSite: structure-based prediction of protein-ligand binding sites. Nucleic Acids Res 2022;50:W13-W20. [PMID: 35412635 PMCID: PMC9252821 DOI: 10.1093/nar/gkac250] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/13/2022] [Accepted: 04/03/2022] [Indexed: 01/13/2023]  Open
8
Pascarelli S, Laurino P. Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins. PLoS Comput Biol 2022;18:e1010016. [PMID: 35377869 PMCID: PMC9009777 DOI: 10.1371/journal.pcbi.1010016] [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: 02/23/2022] [Revised: 04/14/2022] [Accepted: 03/12/2022] [Indexed: 11/25/2022]  Open
9
Exploiting protein family and protein network data to identify novel drug targets for bladder cancer. Oncotarget 2022;13:105-117. [PMID: 35035776 PMCID: PMC8758182 DOI: 10.18632/oncotarget.28175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/08/2021] [Indexed: 12/11/2022]  Open
10
Pazos F. Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity. Bioengineering (Basel) 2021;8:bioengineering8120201. [PMID: 34940354 PMCID: PMC8698372 DOI: 10.3390/bioengineering8120201] [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: 10/26/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022]  Open
11
TwinCons: Conservation score for uncovering deep sequence similarity and divergence. PLoS Comput Biol 2021;17:e1009541. [PMID: 34714829 PMCID: PMC8580257 DOI: 10.1371/journal.pcbi.1009541] [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: 04/16/2021] [Revised: 11/10/2021] [Accepted: 10/06/2021] [Indexed: 11/19/2022]  Open
12
Etzion-Fuchs A, Todd DA, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res 2021;49:e78. [PMID: 33999210 PMCID: PMC8287948 DOI: 10.1093/nar/gkab356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/30/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023]  Open
13
Rauer C, Sen N, Waman VP, Abbasian M, Orengo CA. Computational approaches to predict protein functional families and functional sites. Curr Opin Struct Biol 2021;70:108-122. [PMID: 34225010 DOI: 10.1016/j.sbi.2021.05.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 01/06/2023]
14
Karakulak T, Rifaioglu AS, Rodrigues JPGLM, Karaca E. Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl. Front Mol Biosci 2021;8:658906. [PMID: 34195226 PMCID: PMC8236827 DOI: 10.3389/fmolb.2021.658906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/20/2021] [Indexed: 11/22/2022]  Open
15
Das S, Scholes HM, Sen N, Orengo C. CATH functional families predict functional sites in proteins. Bioinformatics 2021;37:1099-1106. [PMID: 33135053 PMCID: PMC8150129 DOI: 10.1093/bioinformatics/btaa937] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/30/2020] [Accepted: 10/27/2020] [Indexed: 01/12/2023]  Open
16
Pitarch B, Ranea JAG, Pazos F. Protein residues determining interaction specificity in paralogous families. Bioinformatics 2021;37:1076-1082. [PMID: 33135068 DOI: 10.1093/bioinformatics/btaa934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023]  Open
17
Littmann M, Bordin N, Heinzinger M, Schütze K, Dallago C, Orengo C, Rost B. Clustering FunFams using sequence embeddings improves EC purity. Bioinformatics 2021;37:3449-3455. [PMID: 33978744 PMCID: PMC8545299 DOI: 10.1093/bioinformatics/btab371] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/02/2021] [Accepted: 05/11/2021] [Indexed: 12/05/2022]  Open
18
Analysis of Sequence Divergence in Mammalian ABCGs Predicts a Structural Network of Residues That Underlies Functional Divergence. Int J Mol Sci 2021;22:ijms22063012. [PMID: 33809494 PMCID: PMC8001107 DOI: 10.3390/ijms22063012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022]  Open
19
Assessing Protein Function Through Structural Similarities with CATH. Methods Mol Biol 2021. [PMID: 32006277 DOI: 10.1007/978-1-0716-0270-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
20
Bradley D, Viéitez C, Rajeeve V, Selkrig J, Cutillas PR, Beltrao P. Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases. Cell Rep 2021;34:108602. [PMID: 33440154 PMCID: PMC7809594 DOI: 10.1016/j.celrep.2020.108602] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/03/2020] [Accepted: 12/14/2020] [Indexed: 01/04/2023]  Open
21
Alexander MR, Schoeder CT, Brown JA, Smart CD, Moth C, Wikswo JP, Capra JA, Meiler J, Chen W, Madhur MS. Predicting susceptibility to SARS-CoV-2 infection based on structural differences in ACE2 across species. FASEB J 2020;34:15946-15960. [PMID: 33015868 PMCID: PMC7675292 DOI: 10.1096/fj.202001808r] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022]
22
Alexander MR, Schoeder CT, Brown JA, Smart CD, Moth C, Wikswo JP, Capra JA, Meiler J, Chen W, Madhur MS. Which animals are at risk? Predicting species susceptibility to Covid-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32676592 DOI: 10.1101/2020.07.09.194563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
23
Sergeeva AP, Katsamba PS, Cosmanescu F, Brewer JJ, Ahlsen G, Mannepalli S, Shapiro L, Honig B. DIP/Dpr interactions and the evolutionary design of specificity in protein families. Nat Commun 2020;11:2125. [PMID: 32358559 PMCID: PMC7195491 DOI: 10.1038/s41467-020-15981-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/06/2020] [Indexed: 01/10/2023]  Open
24
Marcus K, Mattos C. Water in Ras Superfamily Evolution. J Comput Chem 2020;41:402-414. [PMID: 31483874 DOI: 10.1002/jcc.26060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/17/2019] [Accepted: 08/16/2019] [Indexed: 01/14/2023]
25
Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity. Sci Rep 2020;10:1691. [PMID: 32015389 PMCID: PMC6997377 DOI: 10.1038/s41598-019-55118-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/23/2019] [Indexed: 01/03/2023]  Open
26
Wang J, Yang B, Leier A, Marquez-Lago TT, Hayashida M, Rocker A, Zhang Y, Akutsu T, Chou KC, Strugnell RA, Song J, Lithgow T. Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinformatics 2019;34:2546-2555. [PMID: 29547915 DOI: 10.1093/bioinformatics/bty155] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/09/2018] [Indexed: 12/28/2022]  Open
27
Gazara RK, Moharana KC, Bellieny-Rabelo D, Venancio TM. Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants. PLANT MOLECULAR BIOLOGY 2018;97:435-449. [PMID: 29956113 DOI: 10.1007/s11103-018-0750-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/14/2018] [Indexed: 05/13/2023]
28
Han M, Song Y, Qian J, Ming D. Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database. BMC Bioinformatics 2018;19:204. [PMID: 29859055 PMCID: PMC5984826 DOI: 10.1186/s12859-018-2206-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 05/15/2018] [Indexed: 01/16/2023]  Open
29
Garrido-Martín D, Pazos F. Effect of the sequence data deluge on the performance of methods for detecting protein functional residues. BMC Bioinformatics 2018;19:67. [PMID: 29482506 PMCID: PMC5827975 DOI: 10.1186/s12859-018-2084-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/21/2018] [Indexed: 11/10/2022]  Open
30
Kalaivani R, Reema R, Srinivasan N. Recognition of sites of functional specialisation in all known eukaryotic protein kinase families. PLoS Comput Biol 2018;14:e1005975. [PMID: 29438395 PMCID: PMC5826538 DOI: 10.1371/journal.pcbi.1005975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 02/26/2018] [Accepted: 01/13/2018] [Indexed: 11/25/2022]  Open
31
Neuwald AF, Aravind L, Altschul SF. Inferring joint sequence-structural determinants of protein functional specificity. eLife 2018;7. [PMID: 29336305 PMCID: PMC5770160 DOI: 10.7554/elife.29880] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/22/2017] [Indexed: 01/05/2023]  Open
32
Sánchez-Gracia A, Guirao-Rico S, Hinojosa-Alvarez S, Rozas J. Computational prediction of the phenotypic effects of genetic variants: basic concepts and some application examples in Drosophila nervous system genes. J Neurogenet 2017;31:307-319. [DOI: 10.1080/01677063.2017.1398241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
33
Slama P. Two-domain analysis of JmjN-JmjC and PHD-JmjC lysine demethylases: Detecting an inter-domain evolutionary stress. Proteins 2017;86:3-12. [PMID: 28975662 DOI: 10.1002/prot.25394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/26/2017] [Accepted: 10/03/2017] [Indexed: 11/09/2022]
34
Anderson KA, Huynh FK, Fisher-Wellman K, Stuart JD, Peterson BS, Douros JD, Wagner GR, Thompson JW, Madsen AS, Green MF, Sivley RM, Ilkayeva OR, Stevens RD, Backos DS, Capra JA, Olsen CA, Campbell JE, Muoio DM, Grimsrud PA, Hirschey MD. SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion. Cell Metab 2017;25:838-855.e15. [PMID: 28380376 PMCID: PMC5444661 DOI: 10.1016/j.cmet.2017.03.003] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 09/26/2016] [Accepted: 03/06/2017] [Indexed: 01/17/2023]
35
CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences. Methods Mol Biol 2017;1558:79-110. [PMID: 28150234 DOI: 10.1007/978-1-4939-6783-4_4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
36
Neuwald AF, Altschul SF. Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations. PLoS Comput Biol 2016;12:e1005294. [PMID: 28002465 PMCID: PMC5225019 DOI: 10.1371/journal.pcbi.1005294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 01/10/2017] [Accepted: 12/08/2016] [Indexed: 11/25/2022]  Open
37
Singh C, Glaab E, Linster CL. Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. J Biol Chem 2016;292:1005-1028. [PMID: 27909055 DOI: 10.1074/jbc.m116.760744] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/29/2016] [Indexed: 12/13/2022]  Open
38
Bhadola P, Deo N. Targeting functional motifs of a protein family. Phys Rev E 2016;94:042409. [PMID: 27841537 DOI: 10.1103/physreve.94.042409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 11/07/2022]
39
Sloutsky R, Naegle KM. High-Resolution Identification of Specificity Determining Positions in the LacI Protein Family Using Ensembles of Sub-Sampled Alignments. PLoS One 2016;11:e0162579. [PMID: 27681038 PMCID: PMC5040260 DOI: 10.1371/journal.pone.0162579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/08/2016] [Indexed: 01/24/2023]  Open
40
Moll M, Finn PW, Kavraki LE. Structure-guided selection of specificity determining positions in the human Kinome. BMC Genomics 2016;17 Suppl 4:431. [PMID: 27556159 PMCID: PMC5001202 DOI: 10.1186/s12864-016-2790-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]  Open
41
Boari de Lima E, Meira W, de Melo-Minardi RC. Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering. PLoS Comput Biol 2016;12:e1005001. [PMID: 27348631 PMCID: PMC4922564 DOI: 10.1371/journal.pcbi.1005001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 05/22/2016] [Indexed: 01/14/2023]  Open
42
Lee D, Das S, Dawson NL, Dobrijevic D, Ward J, Orengo C. Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases. PLoS Comput Biol 2016;12:e1004926. [PMID: 27332861 PMCID: PMC4917113 DOI: 10.1371/journal.pcbi.1004926] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/19/2016] [Indexed: 11/23/2022]  Open
43
Huang Y, Wang X, Ge S, Rao GY. Divergence and adaptive evolution of the gibberellin oxidase genes in plants. BMC Evol Biol 2015;15:207. [PMID: 26416509 PMCID: PMC4587577 DOI: 10.1186/s12862-015-0490-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/17/2015] [Indexed: 11/10/2022]  Open
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Chagoyen M, García-Martín JA, Pazos F. Practical analysis of specificity-determining residues in protein families. Brief Bioinform 2015;17:255-61. [DOI: 10.1093/bib/bbv045] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/15/2015] [Indexed: 12/17/2022]  Open
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Das S, Lee D, Sillitoe I, Dawson NL, Lees JG, Orengo CA. Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. Bioinformatics 2015;31:3460-7. [PMID: 26139634 PMCID: PMC4612221 DOI: 10.1093/bioinformatics/btv398] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 06/24/2015] [Indexed: 11/18/2022]  Open
46
Revuelta MV, van Kan JAL, Kay J, Ten Have A. Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes. Genome Biol Evol 2015;6:1480-94. [PMID: 24869856 PMCID: PMC4079213 DOI: 10.1093/gbe/evu110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
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Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA. CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res 2015;43:D376-81. [PMID: 25348408 PMCID: PMC4384018 DOI: 10.1093/nar/gku947] [Citation(s) in RCA: 309] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 09/29/2014] [Indexed: 11/19/2022]  Open
48
Lee TW, Yang ASP, Brittain T, Birch NP. An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: application to neuroserpin reveals regions that differentially regulate inhibitory activity. Proteins 2015;83:135-52. [PMID: 25363759 DOI: 10.1002/prot.24711] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 10/22/2014] [Accepted: 10/27/2014] [Indexed: 01/12/2023]
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Andreani J, Guerois R. Evolution of protein interactions: From interactomes to interfaces. Arch Biochem Biophys 2014;554:65-75. [DOI: 10.1016/j.abb.2014.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/28/2014] [Accepted: 05/12/2014] [Indexed: 12/16/2022]
50
Pappalardo M, Wass MN. VarMod: modelling the functional effects of non-synonymous variants. Nucleic Acids Res 2014;42:W331-6. [PMID: 24906884 PMCID: PMC4086131 DOI: 10.1093/nar/gku483] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
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