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For: Al-Bluwi I, Vaisset M, Siméon T, Cortés J. Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods. BMC Struct Biol 2013;13 Suppl 1:S2. [PMID: 24564964 PMCID: PMC3953241 DOI: 10.1186/1472-6807-13-s1-s2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Number Cited by Other Article(s)
1
Nakao A, Harabuchi Y, Maeda S, Tsuda K. Leveraging algorithmic search in quantum chemical reaction path finding. Phys Chem Chem Phys 2022;24:10305-10310. [PMID: 35437567 DOI: 10.1039/d2cp01079h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
2
Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes. Int J Mol Sci 2021;22:ijms221910501. [PMID: 34638837 PMCID: PMC8508695 DOI: 10.3390/ijms221910501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/18/2021] [Accepted: 09/26/2021] [Indexed: 02/01/2023]  Open
3
Afrasiabi F, Dehghanpoor R, Haspel N. Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC. Molecules 2021;26:molecules26082329. [PMID: 33923805 PMCID: PMC8073574 DOI: 10.3390/molecules26082329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/16/2022]  Open
4
ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths. J Comput Aided Mol Des 2019;33:705-727. [PMID: 31435895 DOI: 10.1007/s10822-019-00216-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022]
5
Morris D, Maximova T, Plaku E, Shehu A. Attenuating dependence on structural data in computing protein energy landscapes. BMC Bioinformatics 2019;20:280. [PMID: 31167640 PMCID: PMC6551245 DOI: 10.1186/s12859-019-2822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
6
Shao Q, Zhu W. Ligand binding effects on the activation of the EGFR extracellular domain. Phys Chem Chem Phys 2019;21:8141-8151. [PMID: 30933195 DOI: 10.1039/c8cp07496h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
7
Sorzano COS, Jiménez A, Mota J, Vilas JL, Maluenda D, Martínez M, Ramírez-Aportela E, Majtner T, Segura J, Sánchez-García R, Rancel Y, del Caño L, Conesa P, Melero R, Jonic S, Vargas J, Cazals F, Freyberg Z, Krieger J, Bahar I, Marabini R, Carazo JM. Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy. Acta Crystallogr F Struct Biol Commun 2019;75:19-32. [PMID: 30605122 PMCID: PMC6317454 DOI: 10.1107/s2053230x18015108] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/26/2018] [Indexed: 11/10/2022]  Open
8
Mechanical variations in proteins with large-scale motions highlight the formation of structural locks. J Struct Biol 2018;203:195-204. [DOI: 10.1016/j.jsb.2018.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
9
Fonseca R, Budday D, van den Bedem H. Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces. J Comput Chem 2018;39:711-720. [PMID: 29315667 DOI: 10.1002/jcc.25138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 11/22/2017] [Accepted: 11/27/2017] [Indexed: 12/22/2022]
10
Nguyen MK, Jaillet L, Redon S. ART-RRT: As-Rigid-As-Possible exploration of ligand unbinding pathways. J Comput Chem 2018;39:665-678. [DOI: 10.1002/jcc.25132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/30/2017] [Accepted: 11/20/2017] [Indexed: 01/09/2023]
11
Abella JR, Moll M, Kavraki LE. Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods. J Comput Biol 2018;25:3-20. [PMID: 29035572 PMCID: PMC5756939 DOI: 10.1089/cmb.2017.0164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
12
Maximova T, Zhang Z, Carr DB, Plaku E, Shehu A. Sample-Based Models of Protein Energy Landscapes and Slow Structural Rearrangements. J Comput Biol 2018;25:33-50. [DOI: 10.1089/cmb.2017.0158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
13
Haspel N, Luo D, González E. Detecting intermediate protein conformations using algebraic topology. BMC Bioinformatics 2017;18:502. [PMID: 29244007 PMCID: PMC5731496 DOI: 10.1186/s12859-017-1918-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
14
Budday D, Fonseca R, Leyendecker S, van den Bedem H. Frustration-guided motion planning reveals conformational transitions in proteins. Proteins 2017;85:1795-1807. [DOI: 10.1002/prot.25333] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/19/2017] [Accepted: 06/07/2017] [Indexed: 01/27/2023]
15
Sapin E, Carr DB, De Jong KA, Shehu A. Computing energy landscape maps and structural excursions of proteins. BMC Genomics 2016;17 Suppl 4:546. [PMID: 27535545 PMCID: PMC5001232 DOI: 10.1186/s12864-016-2798-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
16
Kurkcuoglu Z, Bahar I, Doruker P. ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution. J Chem Theory Comput 2016;12:4549-62. [PMID: 27494296 DOI: 10.1021/acs.jctc.6b00319] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
17
Ekenna C, Thomas S, Amato NM. Adaptive local learning in sampling based motion planning for protein folding. BMC SYSTEMS BIOLOGY 2016;10 Suppl 2:49. [PMID: 27490494 PMCID: PMC4977477 DOI: 10.1186/s12918-016-0297-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
18
Kurkcuoglu Z, Doruker P. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins. PLoS One 2016;11:e0158063. [PMID: 27348230 PMCID: PMC4922591 DOI: 10.1371/journal.pone.0158063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/09/2016] [Indexed: 01/03/2023]  Open
19
Influence of model resolution on geometric simulations of antibody aggregation. ROBOTICA 2016. [DOI: 10.1017/s0263574716000199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
20
Fonseca R, van den Bedem H, Bernauer J. Probing RNA Native Conformational Ensembles with Structural Constraints. J Comput Biol 2016;23:362-71. [PMID: 27028235 DOI: 10.1089/cmb.2015.0201] [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] [Indexed: 12/25/2022]  Open
21
Molloy K, Shehu A. A General, Adaptive, Roadmap-Based Algorithm for Protein Motion Computation. IEEE Trans Nanobioscience 2016;15:158-65. [PMID: 26863668 DOI: 10.1109/tnb.2016.2519246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
22
Shao Q. Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions. Phys Chem Chem Phys 2016;18:29170-29182. [DOI: 10.1039/c6cp05634b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
23
Ceres N, Lavery R. Improving the treatment of coarse-grain electrostatics: CVCEL. J Chem Phys 2015;143:243118. [DOI: 10.1063/1.4933434] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
24
A stochastic roadmap method to model protein structural transitions. ROBOTICA 2015. [DOI: 10.1017/s0263574715001058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
25
Pérez S, Tvaroška I. Carbohydrate-protein interactions: molecular modeling insights. Adv Carbohydr Chem Biochem 2015;71:9-136. [PMID: 25480504 DOI: 10.1016/b978-0-12-800128-8.00001-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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