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For: Silvestre-Ryan J, Lin Y, Chu JW. "Fluctuograms" reveal the intermittent intra-protein communication in subtilisin Carlsberg and correlate mechanical coupling with co-evolution. PLoS Comput Biol 2011;7:e1002023. [PMID: 21455286 PMCID: PMC3063751 DOI: 10.1371/journal.pcbi.1002023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 02/13/2011] [Indexed: 11/21/2022]  Open
Number Cited by Other Article(s)
1
Yu CC, Raj N, Chu JW. Statistical Learning of Protein Elastic Network from Positional Covariance Matrix. Comput Struct Biotechnol J 2023;21:2524-2535. [PMID: 37095762 PMCID: PMC10121796 DOI: 10.1016/j.csbj.2023.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023]  Open
2
Yu CC, Raj N, Chu JW. Edge weights in a protein elastic network reorganize collective motions and render long-range sensitivity responses. J Chem Phys 2022;156:245105. [DOI: 10.1063/5.0095107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
3
Chen YT, Yang H, Chu JW. Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids. Chem Sci 2020;11:4969-4979. [PMID: 34122953 PMCID: PMC8159235 DOI: 10.1039/d0sc00480d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
4
Ciepluch K, Radulescu A, Hoffmann I, Raba A, Allgaier J, Richter D, Biehl R. Influence of PEGylation on Domain Dynamics of Phosphoglycerate Kinase: PEG Acts Like Entropic Spring for the Protein. Bioconjug Chem 2018;29:1950-1960. [DOI: 10.1021/acs.bioconjchem.8b00203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
5
Chu JW, Yang H. Identifying the structural and kinetic elements in protein large-amplitude conformational motions. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1283885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
6
Sang P, Du X, Yang LQ, Meng ZH, Liu SQ. Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: a comparative molecular dynamics simulation study and the underlying mechanisms. RSC Adv 2017. [DOI: 10.1039/c6ra23230b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
7
Click TH, Raj N, Chu JW. Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics Simulation. Methods Enzymol 2016;578:327-42. [PMID: 27497173 DOI: 10.1016/bs.mie.2016.05.024] [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: 02/18/2023]
8
Zhang W, Zhai L, Lu W, Boohaker RJ, Padmalayam I, Li Y. Discovery of Novel Allosteric Eg5 Inhibitors Through Structure-Based Virtual Screening. Chem Biol Drug Des 2016;88:178-87. [PMID: 26864917 DOI: 10.1111/cbdd.12744] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/08/2015] [Accepted: 01/31/2016] [Indexed: 12/11/2022]
9
Tiberti M, Invernizzi G, Papaleo E. (Dis)similarity Index To Compare Correlated Motions in Molecular Simulations. J Chem Theory Comput 2015;11:4404-14. [PMID: 26575932 DOI: 10.1021/acs.jctc.5b00512] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
10
Emerging computational approaches for the study of protein allostery. Arch Biochem Biophys 2013;538:6-15. [DOI: 10.1016/j.abb.2013.07.025] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/23/2013] [Accepted: 07/30/2013] [Indexed: 12/12/2022]
11
Lin Y, Beckham GT, Himmel ME, Crowley MF, Chu JW. Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures. J Phys Chem B 2013;117:10750-8. [PMID: 23972069 DOI: 10.1021/jp405897q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
12
How phosphorylation activates the protein phosphatase-1 • inhibitor-2 complex. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013;1834:71-86. [DOI: 10.1016/j.bbapap.2012.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 08/28/2012] [Accepted: 09/05/2012] [Indexed: 11/16/2022]
13
Papaleo E, Casiraghi N, Arrigoni A, Vanoni M, Coccetti P, De Gioia L. Loop 7 of E2 enzymes: an ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade. PLoS One 2012;7:e40786. [PMID: 22815819 PMCID: PMC3399832 DOI: 10.1371/journal.pone.0040786] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 06/12/2012] [Indexed: 12/31/2022]  Open
14
Pasi M, Tiberti M, Arrigoni A, Papaleo E. xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures. J Chem Inf Model 2012;52:1865-74. [PMID: 22721491 DOI: 10.1021/ci300213c] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
15
Dynamic prestress in a globular protein. PLoS Comput Biol 2012;8:e1002509. [PMID: 22589712 PMCID: PMC3349725 DOI: 10.1371/journal.pcbi.1002509] [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: 09/22/2011] [Accepted: 03/21/2012] [Indexed: 01/15/2023]  Open
16
Papaleo E, Renzetti G, Tiberti M. Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation. PLoS One 2012;7:e35686. [PMID: 22558199 PMCID: PMC3338720 DOI: 10.1371/journal.pone.0035686] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 03/21/2012] [Indexed: 11/25/2022]  Open
17
Papaleo E, Lindorff-Larsen K, De Gioia L. Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation. Phys Chem Chem Phys 2012;14:12515-25. [DOI: 10.1039/c2cp41224a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
18
Lin Y, Silvestre-Ryan J, Himmel ME, Crowley MF, Beckham GT, Chu JW. Protein Allostery at the Solid–Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft. J Am Chem Soc 2011;133:16617-24. [DOI: 10.1021/ja206692g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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