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For: Andreeva A, Prlić A, Hubbard TJP, Murzin AG. SISYPHUS--structural alignments for proteins with non-trivial relationships. Nucleic Acids Res 2006;35:D253-9. [PMID: 17068077 PMCID: PMC1635320 DOI: 10.1093/nar/gkl746] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
Number Cited by Other Article(s)
1
Cretin G, Périn C, Zimmermann N, Galochkina T, Gelly JC. ICARUS: flexible protein structural alignment based on Protein Units. Bioinformatics 2023;39:btad459. [PMID: 37498544 PMCID: PMC10400377 DOI: 10.1093/bioinformatics/btad459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 07/04/2023] [Accepted: 07/26/2023] [Indexed: 07/28/2023]  Open
2
Jayaraman V, Toledo‐Patiño S, Noda‐García L, Laurino P. Mechanisms of protein evolution. Protein Sci 2022;31:e4362. [PMID: 35762715 PMCID: PMC9214755 DOI: 10.1002/pro.4362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/06/2022]
3
Daniluk P, Oleniecki T, Lesyng B. DAMA: a method for computing multiple alignments of protein structures using local structure descriptors. Bioinformatics 2021;38:80-85. [PMID: 34396393 PMCID: PMC8696102 DOI: 10.1093/bioinformatics/btab571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/31/2021] [Accepted: 08/12/2021] [Indexed: 02/03/2023]  Open
4
Talibart H, Coste F. PPalign: optimal alignment of Potts models representing proteins with direct coupling information. BMC Bioinformatics 2021;22:317. [PMID: 34112081 PMCID: PMC8191105 DOI: 10.1186/s12859-021-04222-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/25/2021] [Indexed: 11/29/2022]  Open
5
Le HT, Do PC, Le L. Grafting Methionine on 1F1 Ab Increases the Broad-Activity on HA Structural-Conserved Residues of H1, H2, and H3 Influenza a Viruses. Evol Bioinform Online 2021;17:11769343211003082. [PMID: 33795930 PMCID: PMC7975486 DOI: 10.1177/11769343211003082] [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: 11/05/2020] [Accepted: 02/24/2021] [Indexed: 11/27/2022]  Open
6
Searching protein space for ancient sub-domain segments. Curr Opin Struct Biol 2021;68:105-112. [PMID: 33476896 DOI: 10.1016/j.sbi.2020.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/29/2020] [Indexed: 01/08/2023]
7
Carpentier M, Chomilier J. Protein multiple alignments: sequence-based versus structure-based programs. Bioinformatics 2020;35:3970-3980. [PMID: 30942864 DOI: 10.1093/bioinformatics/btz236] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/05/2019] [Accepted: 04/02/2019] [Indexed: 11/14/2022]  Open
8
Rozewicki J, Li S, Amada KM, Standley DM, Katoh K. MAFFT-DASH: integrated protein sequence and structural alignment. Nucleic Acids Res 2019;47:W5-W10. [PMID: 31062021 PMCID: PMC6602451 DOI: 10.1093/nar/gkz342] [Citation(s) in RCA: 242] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/07/2019] [Accepted: 04/25/2019] [Indexed: 12/22/2022]  Open
9
Nute M, Saleh E, Warnow T. Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets. Syst Biol 2019;68:396-411. [PMID: 30329135 PMCID: PMC6472439 DOI: 10.1093/sysbio/syy068] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/27/2018] [Accepted: 10/11/2018] [Indexed: 01/15/2023]  Open
10
RUPEE: A fast and accurate purely geometric protein structure search. PLoS One 2019;14:e0213712. [PMID: 30875409 PMCID: PMC6420038 DOI: 10.1371/journal.pone.0213712] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/27/2019] [Indexed: 11/19/2022]  Open
11
Alva V, Söding J, Lupas AN. A vocabulary of ancient peptides at the origin of folded proteins. eLife 2015;4:e09410. [PMID: 26653858 PMCID: PMC4739770 DOI: 10.7554/elife.09410] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 12/13/2015] [Indexed: 01/01/2023]  Open
12
Terashi G, Takeda-Shitaka M. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area. PLoS One 2015;10:e0141440. [PMID: 26502070 PMCID: PMC4621035 DOI: 10.1371/journal.pone.0141440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 10/08/2015] [Indexed: 12/26/2022]  Open
13
Goncearenco A, Berezovsky IN. Protein function from its emergence to diversity in contemporary proteins. Phys Biol 2015;12:045002. [PMID: 26057563 DOI: 10.1088/1478-3975/12/4/045002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
14
Global view of the protein universe. Proc Natl Acad Sci U S A 2014;111:11691-6. [PMID: 25071170 DOI: 10.1073/pnas.1403395111] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
15
Kopec KO, Lupas AN. β-Propeller blades as ancestral peptides in protein evolution. PLoS One 2013;8:e77074. [PMID: 24143202 PMCID: PMC3797127 DOI: 10.1371/journal.pone.0077074] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/05/2013] [Indexed: 12/04/2022]  Open
16
Topham CM, Rouquier M, Tarrat N, André I. Adaptive Smith-Waterman residue match seeding for protein structural alignment. Proteins 2013;81:1823-39. [DOI: 10.1002/prot.24327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/22/2013] [Accepted: 05/15/2013] [Indexed: 12/30/2022]
17
Kolodny R, Pereyaslavets L, Samson AO, Levitt M. On the Universe of Protein Folds. Annu Rev Biophys 2013;42:559-82. [DOI: 10.1146/annurev-biophys-083012-130432] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
18
Minami S, Sawada K, Chikenji G. MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models, Alternative alignments, and Non-sequential alignments. BMC Bioinformatics 2013;14:24. [PMID: 23331634 PMCID: PMC3637537 DOI: 10.1186/1471-2105-14-24] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 01/08/2013] [Indexed: 11/10/2022]  Open
19
Wohlers I, Andonov R, Klau GW. DALIX: optimal DALI protein structure alignment. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013;10:26-36. [PMID: 23702541 DOI: 10.1109/tcbb.2012.143] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
20
Arriagada M, Poleksic A. On the difference in quality between current heuristic and optimal solutions to the protein structure alignment problem. BIOMED RESEARCH INTERNATIONAL 2012;2013:459248. [PMID: 23509725 PMCID: PMC3591119 DOI: 10.1155/2013/459248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 11/02/2012] [Indexed: 11/17/2022]
21
Shih HH, Tu C, Cao W, Klein A, Ramsey R, Fennell BJ, Lambert M, Ní Shúilleabháin D, Autin B, Kouranova E, Laxmanan S, Braithwaite S, Wu L, Ait-Zahra M, Milici AJ, Dumin JA, LaVallie ER, Arai M, Corcoran C, Paulsen JE, Gill D, Cunningham O, Bard J, Mosyak L, Finlay WJJ. An ultra-specific avian antibody to phosphorylated tau protein reveals a unique mechanism for phosphoepitope recognition. J Biol Chem 2012;287:44425-34. [PMID: 23148212 DOI: 10.1074/jbc.m112.415935] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
22
Wohlers I, Malod-Dognin N, Andonov R, Klau GW. CSA: comprehensive comparison of pairwise protein structure alignments. Nucleic Acids Res 2012;40:W303-9. [PMID: 22553365 PMCID: PMC3394275 DOI: 10.1093/nar/gks362] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/29/2012] [Accepted: 04/10/2012] [Indexed: 11/23/2022]  Open
23
Bliven S, Prlić A. Circular permutation in proteins. PLoS Comput Biol 2012;8:e1002445. [PMID: 22496628 PMCID: PMC3320104 DOI: 10.1371/journal.pcbi.1002445] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
24
Kovalchuk N, Smith J, Bazanova N, Pyvovarenko T, Singh R, Shirley N, Ismagul A, Johnson A, Milligan AS, Hrmova M, Langridge P, Lopato S. Characterization of the wheat gene encoding a grain-specific lipid transfer protein TdPR61, and promoter activity in wheat, barley and rice. JOURNAL OF EXPERIMENTAL BOTANY 2012;63:2025-40. [PMID: 22213809 DOI: 10.1093/jxb/err409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
25
Andreeva A. Classification of proteins: available structural space for molecular modeling. Methods Mol Biol 2012;857:1-31. [PMID: 22323215 DOI: 10.1007/978-1-61779-588-6_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
26
Sun H, Sacan A, Ferhatosmanoglu H, Wang Y. Smolign: a spatial motifs-based protein multiple structural alignment method. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012;9:249-261. [PMID: 21464513 DOI: 10.1109/tcbb.2011.67] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
27
Use of comparative genomics approaches to characterize interspecies differences in response to environmental chemicals: challenges, opportunities, and research needs. Toxicol Appl Pharmacol 2011;271:372-85. [PMID: 22142766 DOI: 10.1016/j.taap.2011.11.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 11/11/2011] [Accepted: 11/16/2011] [Indexed: 01/12/2023]
28
SALEM SAEED, ZAKI MOHAMMEDJ, BYSTROFF CHRISTOPHER. ITERATIVE NON-SEQUENTIAL PROTEIN STRUCTURAL ALIGNMENT. J Bioinform Comput Biol 2011;7:571-96. [PMID: 19507290 DOI: 10.1142/s0219720009004205] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 11/05/2008] [Accepted: 11/06/2008] [Indexed: 11/18/2022]
29
Daniluk P, Lesyng B. A novel method to compare protein structures using local descriptors. BMC Bioinformatics 2011;12:344. [PMID: 21849047 PMCID: PMC3179968 DOI: 10.1186/1471-2105-12-344] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Accepted: 08/17/2011] [Indexed: 11/15/2022]  Open
30
Nguyen MN, Tan KP, Madhusudhan MS. CLICK--topology-independent comparison of biomolecular 3D structures. Nucleic Acids Res 2011;39:W24-8. [PMID: 21602266 PMCID: PMC3125785 DOI: 10.1093/nar/gkr393] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Revised: 04/19/2011] [Accepted: 05/03/2011] [Indexed: 01/28/2023]  Open
31
Rocha J, Alberich R. The significance of the ProtDeform score for structure prediction and alignment. PLoS One 2011;6:e20889. [PMID: 21738592 PMCID: PMC3125161 DOI: 10.1371/journal.pone.0020889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/12/2011] [Indexed: 11/21/2022]  Open
32
Nguyen MN, Madhusudhan MS. Biological insights from topology independent comparison of protein 3D structures. Nucleic Acids Res 2011;39:e94. [PMID: 21596786 PMCID: PMC3152366 DOI: 10.1093/nar/gkr348] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
33
Venkateswaran JG, Song B, Kahveci T, Jermaine C. TRIAL: a tool for finding distant structural similarities. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011;8:819-831. [PMID: 21393655 DOI: 10.1109/tcbb.2009.28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
34
Goncearenco A, Berezovsky IN. Prototypes of elementary functional loops unravel evolutionary connections between protein functions. ACTA ACUST UNITED AC 2010;26:i497-503. [PMID: 20823313 PMCID: PMC2935408 DOI: 10.1093/bioinformatics/btq374] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
35
Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE. Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics 2010;26:2983-5. [PMID: 20937596 PMCID: PMC3003546 DOI: 10.1093/bioinformatics/btq572] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
36
Andreeva A, Murzin AG. Structural classification of proteins and structural genomics: new insights into protein folding and evolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010;66:1190-7. [PMID: 20944210 PMCID: PMC2954204 DOI: 10.1107/s1744309110007177] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 02/24/2010] [Indexed: 11/10/2022]
37
Wohlers I, Domingues FS, Klau GW. Towards optimal alignment of protein structure distance matrices. Bioinformatics 2010;26:2273-80. [PMID: 20639543 DOI: 10.1093/bioinformatics/btq420] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
38
Konagurthu AS, Reboul CF, Schmidberger JW, Irving JA, Lesk AM, Stuckey PJ, Whisstock JC, Buckle AM. MUSTANG-MR structural sieving server: applications in protein structural analysis and crystallography. PLoS One 2010;5:e10048. [PMID: 20386610 PMCID: PMC2850368 DOI: 10.1371/journal.pone.0010048] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 03/16/2010] [Indexed: 11/19/2022]  Open
39
Alva V, Remmert M, Biegert A, Lupas AN, Söding J. A galaxy of folds. Protein Sci 2010;19:124-30. [PMID: 19937658 DOI: 10.1002/pro.297] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
40
Joerger AC, Fersht AR. The tumor suppressor p53: from structures to drug discovery. Cold Spring Harb Perspect Biol 2010;2:a000919. [PMID: 20516128 DOI: 10.1101/cshperspect.a000919] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
41
Berbalk C, Schwaiger CS, Lackner P. Accuracy analysis of multiple structure alignments. Protein Sci 2009;18:2027-35. [PMID: 19621383 DOI: 10.1002/pro.213] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
42
PAUL: protein structural alignment using integer linear programming and Lagrangian relaxation. BMC Bioinformatics 2009. [PMCID: PMC2764133 DOI: 10.1186/1471-2105-10-s13-p2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
43
Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc Natl Acad Sci U S A 2009;106:17377-82. [PMID: 19805138 DOI: 10.1073/pnas.0907971106] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
44
Poleksic A. Algorithms for optimal protein structure alignment. ACTA ACUST UNITED AC 2009;25:2751-6. [PMID: 19734152 DOI: 10.1093/bioinformatics/btp530] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
45
Micheletti C, Orland H. MISTRAL: a tool for energy-based multiple structural alignment of proteins. ACTA ACUST UNITED AC 2009;25:2663-9. [PMID: 19692555 DOI: 10.1093/bioinformatics/btp506] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
46
Sippl MJ. Fold space unlimited. Curr Opin Struct Biol 2009;19:312-20. [DOI: 10.1016/j.sbi.2009.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/16/2009] [Accepted: 03/16/2009] [Indexed: 11/25/2022]
47
Hasegawa H, Holm L. Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol 2009;19:341-8. [PMID: 19481444 DOI: 10.1016/j.sbi.2009.04.003] [Citation(s) in RCA: 303] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 04/16/2009] [Indexed: 11/30/2022]
48
Rocha J, Segura J, Wilson RC, Dasgupta S. Flexible structural protein alignment by a sequence of local transformations. ACTA ACUST UNITED AC 2009;25:1625-31. [PMID: 19417057 PMCID: PMC2940242 DOI: 10.1093/bioinformatics/btp296] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Tidow H, Andreeva A, Rutherford TJ, Fersht AR. Solution structure of the U11-48K CHHC zinc-finger domain that specifically binds the 5' splice site of U12-type introns. Structure 2009;17:294-302. [PMID: 19217400 DOI: 10.1016/j.str.2008.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 11/24/2008] [Accepted: 11/26/2008] [Indexed: 10/21/2022]
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Cradle-loop barrels and the concept of metafolds in protein classification by natural descent. Curr Opin Struct Biol 2008;18:358-65. [DOI: 10.1016/j.sbi.2008.02.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2007] [Accepted: 02/14/2008] [Indexed: 11/19/2022]
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