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For: Carugo O, Argos P. Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors. Proteins 1998. [DOI: 10.1002/(sici)1097-0134(19980501)31:2<201::aid-prot9>3.0.co;2-o] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Number Cited by Other Article(s)
1
Chang F, Liu L, Hu F, Sun X, Zhao Y, Zhang N, Li C. RNAfcg: RNA Flexibility Prediction Based on Topological Centrality and Global Features. J Chem Inf Model 2024;64:7786-7792. [PMID: 39276067 DOI: 10.1021/acs.jcim.4c00848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2024]
2
Xiang X, Zhu E, Xiong D, Wen Y, Xing Y, Yue L, He S, Han N, Huang Z. Improving the Thermostability of Thermomyces lanuginosus Lipase by Restricting the Flexibility of N-Terminus and C-Terminus Simultaneously via the 25-Loop Substitutions. Int J Mol Sci 2023;24:16562. [PMID: 38068886 PMCID: PMC10706272 DOI: 10.3390/ijms242316562] [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: 11/01/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]  Open
3
Hancock JT. Are Protein Cavities and Pockets Commonly Used by Redox Active Signalling Molecules? PLANTS (BASEL, SWITZERLAND) 2023;12:2594. [PMID: 37514209 PMCID: PMC10383989 DOI: 10.3390/plants12142594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
4
Carugo O. Uses and Abuses of the Atomic Displacement Parameters in Structural Biology. Methods Mol Biol 2022;2449:281-298. [PMID: 35507268 DOI: 10.1007/978-1-0716-2095-3_12] [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: 06/14/2023]
5
Random sampling of the Protein Data Bank: RaSPDB. Sci Rep 2021;11:24178. [PMID: 34921198 PMCID: PMC8683422 DOI: 10.1038/s41598-021-03615-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/25/2021] [Indexed: 11/29/2022]  Open
6
Wei H, Wang B, Yang J, Gao J. RNA Flexibility Prediction With Sequence Profile and Predicted Solvent Accessibility. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:2017-2022. [PMID: 31794403 DOI: 10.1109/tcbb.2019.2956496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
7
Xu D, Meisburger SP, Ando N. Correlated Motions in Structural Biology. Biochemistry 2021;60:2331-2340. [PMID: 34291898 DOI: 10.1021/acs.biochem.1c00420] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
8
Gill SC, Mobley DL. Reversibly Sampling Conformations and Binding Modes Using Molecular Darting. J Chem Theory Comput 2021;17:302-314. [PMID: 33289558 PMCID: PMC8121195 DOI: 10.1021/acs.jctc.0c00752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
9
Kanapeckaitė A, Beaurivage C, Hancock M, Verschueren E. Fi-score: a novel approach to characterise protein topology and aid in drug discovery studies. J Biomol Struct Dyn 2020;40:4197-4207. [DOI: 10.1080/07391102.2020.1854859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
10
Brinkjost T, Ehrt C, Koch O, Mutzel P. SCOT: Rethinking the classification of secondary structure elements. Bioinformatics 2020;36:2417-2428. [PMID: 31742326 DOI: 10.1093/bioinformatics/btz826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/02/2019] [Accepted: 11/16/2019] [Indexed: 11/13/2022]  Open
11
Masmaliyeva RC, Babai KH, Murshudov GN. Local and global analysis of macromolecular atomic displacement parameters. Acta Crystallogr D Struct Biol 2020;76:926-937. [PMID: 33021494 PMCID: PMC7543658 DOI: 10.1107/s2059798320011043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/11/2020] [Indexed: 04/13/2023]  Open
12
Han N, Ma Y, Mu Y, Tang X, Li J, Huang Z. Enhancing thermal tolerance of a fungal GH11 xylanase guided by B-factor analysis and multiple sequence alignment. Enzyme Microb Technol 2019;131:109422. [DOI: 10.1016/j.enzmictec.2019.109422] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/24/2019] [Accepted: 09/03/2019] [Indexed: 11/24/2022]
13
Structural Basis for the Regulation of PPARγ Activity by Imatinib. Molecules 2019;24:molecules24193562. [PMID: 31581474 PMCID: PMC6803859 DOI: 10.3390/molecules24193562] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022]  Open
14
Johnson TW, Gallego RA, Brooun A, Gehlhaar D, McTigue M. Reviving B-Factors: Retrospective Normalized B-Factor Analysis of c-ros Oncogene 1 Receptor Tyrosine Kinase and Anaplastic Lymphoma Kinase L1196M with Crizotinib and Lorlatinib. ACS Med Chem Lett 2018;9:878-883. [PMID: 30258534 DOI: 10.1021/acsmedchemlett.8b00147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/18/2018] [Indexed: 11/28/2022]  Open
15
Carugo O. How large B-factors can be in protein crystal structures. BMC Bioinformatics 2018;19:61. [PMID: 29471780 PMCID: PMC5824579 DOI: 10.1186/s12859-018-2083-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/20/2018] [Indexed: 11/29/2022]  Open
16
Guruge I, Taherzadeh G, Zhan J, Zhou Y, Yang Y. B -factor profile prediction for RNA flexibility using support vector machines. J Comput Chem 2017;39:407-411. [DOI: 10.1002/jcc.25124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/07/2017] [Indexed: 12/12/2022]
17
Gaussian network model can be enhanced by combining solvent accessibility in proteins. Sci Rep 2017;7:7486. [PMID: 28790346 PMCID: PMC5548781 DOI: 10.1038/s41598-017-07677-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/29/2017] [Indexed: 01/03/2023]  Open
18
Protein hydration: Investigation of globular protein crystal structures. Int J Biol Macromol 2017;99:160-165. [DOI: 10.1016/j.ijbiomac.2017.02.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/10/2017] [Indexed: 01/06/2023]
19
Han N, Miao H, Ding J, Li J, Mu Y, Zhou J, Huang Z. Improving the thermostability of a fungal GH11 xylanase via site-directed mutagenesis guided by sequence and structural analysis. BIOTECHNOLOGY FOR BIOFUELS 2017;10:133. [PMID: 28546828 PMCID: PMC5442702 DOI: 10.1186/s13068-017-0824-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/17/2017] [Indexed: 05/28/2023]
20
Waters in room temperature and cryo protein crystal structures. Z KRIST-CRYST MATER 2016. [DOI: 10.1515/zkri-2016-1986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
21
Carugo O, Djinović-Carugo K. Criteria to Extract High-Quality Protein Data Bank Subsets for Structure Users. Methods Mol Biol 2016;1415:139-152. [PMID: 27115631 DOI: 10.1007/978-1-4939-3572-7_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
22
Statistical survey of the buried waters in the Protein Data Bank. Amino Acids 2015;48:193-202. [PMID: 26315961 DOI: 10.1007/s00726-015-2064-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/29/2015] [Indexed: 12/18/2022]
23
Touw WG, Vriend G. BDB: Databank of PDB files with consistent B-factors. Protein Eng Des Sel 2014;27:457-62. [DOI: 10.1093/protein/gzu044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
24
Carugo O. Buried chloride stereochemistry in the Protein Data Bank. BMC STRUCTURAL BIOLOGY 2014;14:19. [PMID: 25928393 PMCID: PMC4582432 DOI: 10.1186/s12900-014-0019-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/08/2014] [Indexed: 11/11/2022]
25
Colloc'h N, Prangé T. Functional relevance of the internal hydrophobic cavity of urate oxidase. FEBS Lett 2014;588:1715-9. [PMID: 24657440 DOI: 10.1016/j.febslet.2014.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
26
Dynamic void distribution in myoglobin and five mutants. Sci Rep 2014;4:4011. [PMID: 24500195 PMCID: PMC3915302 DOI: 10.1038/srep04011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/16/2014] [Indexed: 11/09/2022]  Open
27
Xia K, Wei GW. Stochastic model for protein flexibility analysis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013;88:062709. [PMID: 24483488 DOI: 10.1103/physreve.88.062709] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/03/2013] [Indexed: 06/03/2023]
28
Biswas M, Dey S, Khamrui S, Sen U, Dasgupta J. Conformational barrier of CheY3 and inability of CheY4 to bind FliM control the flagellar motor action in Vibrio cholerae. PLoS One 2013;8:e73923. [PMID: 24066084 PMCID: PMC3774744 DOI: 10.1371/journal.pone.0073923] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 07/26/2013] [Indexed: 12/22/2022]  Open
29
Liu YY, Shih CH, Hwang JK, Chen CC. Deriving correlated motions in proteins from X-ray structure refinement by using TLS parameters. Gene 2013;518:52-8. [DOI: 10.1016/j.gene.2012.11.086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/27/2012] [Indexed: 12/14/2022]
30
Toward an understanding of the sequence and structural basis of allosteric proteins. J Mol Graph Model 2013;40:30-9. [PMID: 23337573 DOI: 10.1016/j.jmgm.2012.12.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 12/18/2012] [Accepted: 12/19/2012] [Indexed: 11/19/2022]
31
Carugo O, Djinović-Carugo K. How many packing contacts are observed in protein crystals? J Struct Biol 2012;180:96-100. [DOI: 10.1016/j.jsb.2012.05.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 04/03/2012] [Accepted: 05/16/2012] [Indexed: 11/30/2022]
32
Majumder S, Khamrui S, Dasgupta J, Dattagupta JK, Sen U. Role of remote scaffolding residues in the inhibitory loop pre-organization, flexibility, rigidification and enzyme inhibition of serine protease inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012;1824:882-90. [PMID: 22709512 DOI: 10.1016/j.bbapap.2012.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 04/22/2012] [Accepted: 04/23/2012] [Indexed: 11/27/2022]
33
Kirillova S, Carugo O. Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures. BMC STRUCTURAL BIOLOGY 2011;11:41. [PMID: 22011380 PMCID: PMC3206426 DOI: 10.1186/1472-6807-11-41] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 10/19/2011] [Indexed: 11/10/2022]
34
Ünal C, Schwedhelm KF, Thiele A, Weiwad M, Schweimer K, Frese F, Fischer G, Hacker J, Faber C, Steinert M. Collagen IV-derived peptide binds hydrophobic cavity of Legionella pneumophila Mip and interferes with bacterial epithelial transmigration. Cell Microbiol 2011;13:1558-72. [DOI: 10.1111/j.1462-5822.2011.01641.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
35
Bocahut A, Bernad S, Sebban P, Sacquin-Mora S. Frontier Residues Lining Globin Internal Cavities Present Specific Mechanical Properties. J Am Chem Soc 2011;133:8753-61. [DOI: 10.1021/ja202587a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
36
Tian F, Zhang C, Fan X, Yang X, Wang X, Liang H. Predicting the Flexibility Profile of Ribosomal RNAs. Mol Inform 2010;29:707-15. [PMID: 27464014 DOI: 10.1002/minf.201000092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 09/28/2010] [Indexed: 11/06/2022]
37
Ren Y, Chen X, Li X, Lai H, Wang Q, Zhou P, Chen G. Quantitative prediction of the thermal motion and intrinsic disorder of protein cofactors in crystalline state: A case study on halide anions. J Theor Biol 2010;266:291-8. [DOI: 10.1016/j.jtbi.2010.06.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 06/08/2010] [Accepted: 06/25/2010] [Indexed: 10/19/2022]
38
Kuzmanic A, Zagrovic B. Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophys J 2010;98:861-71. [PMID: 20197040 DOI: 10.1016/j.bpj.2009.11.011] [Citation(s) in RCA: 264] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Revised: 10/30/2009] [Accepted: 11/03/2009] [Indexed: 11/19/2022]  Open
39
Montange RK, Mondragón E, van Tyne D, Garst AD, Ceres P, Batey RT. Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J Mol Biol 2009;396:761-72. [PMID: 20006621 DOI: 10.1016/j.jmb.2009.12.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 11/30/2009] [Accepted: 12/06/2009] [Indexed: 12/17/2022]
40
Zhang H, Zhang T, Chen K, Shen S, Ruan J, Kurgan L. On the relation between residue flexibility and local solvent accessibility in proteins. Proteins 2009;76:617-36. [DOI: 10.1002/prot.22375] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
41
Rahman MN, Vlahakis JZ, Vukomanovic D, Szarek WA, Nakatsu K, Jia Z. X-ray Crystal Structure of Human Heme Oxygenase-1 with (2R,4S)-2-[2-(4-Chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4[((5-trifluoromethylpyridin-2-yl)thio)methyl]-1,3-dioxolane: A Novel, Inducible Binding Mode. J Med Chem 2009;52:4946-50. [DOI: 10.1021/jm900434f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
42
Klvana M, Pavlova M, Koudelakova T, Chaloupkova R, Dvorak P, Prokop Z, Stsiapanava A, Kuty M, Kuta-Smatanova I, Dohnalek J, Kulhanek P, Wade RC, Damborsky J. Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations. J Mol Biol 2009;392:1339-56. [PMID: 19577578 DOI: 10.1016/j.jmb.2009.06.076] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 06/25/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
43
Roberts BC, Mancera RL. Ligand-protein docking with water molecules. J Chem Inf Model 2008;48:397-408. [PMID: 18211049 DOI: 10.1021/ci700285e] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
44
Shapovalov MV, Dunbrack RL. Statistical and conformational analysis of the electron density of protein side chains. Proteins 2007;66:279-303. [PMID: 17080462 DOI: 10.1002/prot.21150] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
45
Colloc'h N, Sopkova-de Oliveira Santos J, Retailleau P, Vivarès D, Bonneté F, Langlois d'Estainto B, Gallois B, Brisson A, Risso JJ, Lemaire M, Prangé T, Abraini JH. Protein crystallography under xenon and nitrous oxide pressure: comparison with in vivo pharmacology studies and implications for the mechanism of inhaled anesthetic action. Biophys J 2006;92:217-24. [PMID: 17028130 PMCID: PMC1697869 DOI: 10.1529/biophysj.106.093807] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
46
Hritz J, Zoldák G, Sedlák E. Cofactor assisted gating mechanism in the active site of NADH oxidase from Thermus thermophilus. Proteins 2006;64:465-76. [PMID: 16642502 DOI: 10.1002/prot.20990] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
47
Cojocaru V, Winn PJ, Wade RC. The ins and outs of cytochrome P450s. Biochim Biophys Acta Gen Subj 2006;1770:390-401. [PMID: 16920266 DOI: 10.1016/j.bbagen.2006.07.005] [Citation(s) in RCA: 278] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Accepted: 07/14/2006] [Indexed: 11/17/2022]
48
Yuan Z, Bailey TL, Teasdale RD. Prediction of protein B-factor profiles. Proteins 2006;58:905-12. [PMID: 15645415 DOI: 10.1002/prot.20375] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Schlessinger A, Rost B. Protein flexibility and rigidity predicted from sequence. Proteins 2006;61:115-26. [PMID: 16080156 DOI: 10.1002/prot.20587] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Bhalla J, Storchan GB, MacCarthy CM, Uversky VN, Tcherkasskaya O. Local flexibility in molecular function paradigm. Mol Cell Proteomics 2006;5:1212-23. [PMID: 16571897 DOI: 10.1074/mcp.m500315-mcp200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
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