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For: Baysal C, Atilgan AR. Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2. Proteins 2001;45:62-70. [PMID: 11536361 DOI: 10.1002/prot.1124] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Number Cited by Other Article(s)
1
Berksoz M, Atilgan C. Allosteric modulation of fluorescence revealed by hydrogen bond dynamics in a genetically encoded maltose biosensor. Proteins 2024;92:923-932. [PMID: 38572606 DOI: 10.1002/prot.26688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/02/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
2
Abdizadeh H, Jalalypour F, Atilgan AR, Atilgan C. A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs. Front Mol Biosci 2020;7:210. [PMID: 33195399 PMCID: PMC7477071 DOI: 10.3389/fmolb.2020.00210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/03/2020] [Indexed: 11/13/2022]  Open
3
Abdizadeh H, Atilgan AR, Atilgan C, Dedeoglu B. Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins. Metallomics 2018;9:1513-1533. [PMID: 28967944 DOI: 10.1039/c7mt00216e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
4
Abdizadeh H, Tamer YT, Acar O, Toprak E, Atilgan AR, Atilgan C. Increased substrate affinity in the Escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance. Phys Chem Chem Phys 2018;19:11416-11428. [PMID: 28422217 DOI: 10.1039/c7cp01458a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
5
Computational Methods for Efficient Sampling of Protein Landscapes and Disclosing Allosteric Regions. COMPUTATIONAL MOLECULAR MODELLING IN STRUCTURAL BIOLOGY 2018;113:33-63. [DOI: 10.1016/bs.apcsb.2018.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
6
Li Z, Bolia A, Maxwell JD, Bobkov AA, Ghirlanda G, Ozkan SB, Margulis CJ. A Rigid Hinge Region Is Necessary for High-Affinity Binding of Dimannose to Cyanovirin and Associated Constructs. Biochemistry 2015;54:6951-60. [PMID: 26507789 DOI: 10.1021/acs.biochem.5b00635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
7
Guven G, Atilgan AR, Atilgan C. Protonation States of Remote Residues Affect Binding–Release Dynamics of the Ligand but Not the Conformation of Apo Ferric Binding Protein. J Phys Chem B 2014;118:11677-87. [DOI: 10.1021/jp5079218] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
8
Bayram Akcapinar G, Gul O, Sezerman UO. From in silico to in vitro: Modelling and production of Trichoderma reesei endoglucanase 1 and its mutant in Pichia pastoris. J Biotechnol 2012;159:61-8. [DOI: 10.1016/j.jbiotec.2012.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 01/02/2012] [Accepted: 01/04/2012] [Indexed: 10/28/2022]
9
Atilgan C, Okan OB, Atilgan AR. Network-based models as tools hinting at nonevident protein functionality. Annu Rev Biophys 2012;41:205-25. [PMID: 22404685 DOI: 10.1146/annurev-biophys-050511-102305] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
10
Atilgan AR, Aykut AO, Atilgan C. Subtle pH differences trigger single residue motions for moderating conformations of calmodulin. J Chem Phys 2011;135:155102. [DOI: 10.1063/1.3651807] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
11
Turgut D, Atilgan AR, Atilgan C. Assortative mixing in close-packed spatial networks. PLoS One 2010;5:e15551. [PMID: 21179578 PMCID: PMC3002975 DOI: 10.1371/journal.pone.0015551] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 11/11/2010] [Indexed: 12/02/2022]  Open
12
Atilgan C, Gerek ZN, Ozkan SB, Atilgan AR. Manipulation of conformational change in proteins by single-residue perturbations. Biophys J 2010;99:933-43. [PMID: 20682272 DOI: 10.1016/j.bpj.2010.05.020] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 05/03/2010] [Accepted: 05/07/2010] [Indexed: 11/28/2022]  Open
13
Atilgan C, Atilgan AR. Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein. PLoS Comput Biol 2009;5:e1000544. [PMID: 19851447 PMCID: PMC2758672 DOI: 10.1371/journal.pcbi.1000544] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 09/22/2009] [Indexed: 11/18/2022]  Open
14
A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling. J Comput Aided Mol Des 2008;22:815-29. [PMID: 18465087 DOI: 10.1007/s10822-008-9216-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Accepted: 04/15/2008] [Indexed: 10/22/2022]
15
Boyer JA, Lee AL. Monitoring aromatic picosecond to nanosecond dynamics in proteins via 13C relaxation: expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin c. Biochemistry 2008;47:4876-86. [PMID: 18393447 DOI: 10.1021/bi702330t] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
16
Platform S: Protein Structure and Allosteric Communication. Biophys J 2008. [DOI: 10.1016/s0006-3495(08)79040-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]  Open
17
Atilgan AR, Turgut D, Atilgan C. Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. Biophys J 2007;92:3052-62. [PMID: 17293401 PMCID: PMC1852335 DOI: 10.1529/biophysj.106.099440] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
18
Erman B. The gaussian network model: precise prediction of residue fluctuations and application to binding problems. Biophys J 2006;91:3589-99. [PMID: 16935951 PMCID: PMC1630469 DOI: 10.1529/biophysj.106.090803] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
19
Demirel MC, Cherny D. Clustering and diversity of fluctuations for proteins. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2005;1:41-6. [PMID: 17292056 DOI: 10.1016/j.nano.2004.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2004] [Accepted: 11/25/2004] [Indexed: 05/13/2023]
20
Baysal C, Atilgan AR. Relaxation kinetics and the glassiness of native proteins: coupling of timescales. Biophys J 2004;88:1570-6. [PMID: 15596500 PMCID: PMC1305214 DOI: 10.1529/biophysj.104.050252] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
21
Atilgan AR, Akan P, Baysal C. Small-world communication of residues and significance for protein dynamics. Biophys J 2004;86:85-91. [PMID: 14695252 PMCID: PMC1303839 DOI: 10.1016/s0006-3495(04)74086-2] [Citation(s) in RCA: 191] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
22
Lei H, Smith PE. The Effects of Internal Water Molecules on the Structure and Dynamics of Chymotrypsin Inhibitor 2. J Phys Chem B 2003. [DOI: 10.1021/jp0223105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
23
Baysal C, Atilgan AR. Relaxation kinetics and the glassiness of proteins: the case of bovine pancreatic trypsin inhibitor. Biophys J 2002;83:699-705. [PMID: 12124257 PMCID: PMC1302179 DOI: 10.1016/s0006-3495(02)75201-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
24
Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-43. [PMID: 12001221 DOI: 10.1002/prot.10115] [Citation(s) in RCA: 771] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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