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For: Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S, Xiao X. Biomolecularmodeling and simulation: a field coming of age. Q Rev Biophys 2011;44:191-228. [PMID: 21226976 PMCID: PMC3700731 DOI: 10.1017/s0033583510000284] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Number Cited by Other Article(s)
1
Jin J, Reichman DR. Hierarchical Framework for Predicting Entropies in Bottom-Up Coarse-Grained Models. J Phys Chem B 2024;128:3182-3199. [PMID: 38507575 DOI: 10.1021/acs.jpcb.3c07624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
2
Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024;9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
3
Shakibaie MR, Modaresi F, Azizi O, Tadjrobehkar O, Ghaemi MM. Amphiphilic peptide Mastoparan-B induces conformational changes within the AdeB efflux pump, down-regulates adeB gene expression, and restores antibiotic susceptibility in an MDR strain of Acinetobacter baumannii. Proteins 2023;91:1205-1221. [PMID: 37455426 DOI: 10.1002/prot.26539] [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] [Received: 12/16/2022] [Revised: 05/11/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023]
4
Zhang Y, He L, Li S. Temperature dependence of DNA elasticity: An all-atom molecular dynamics simulation study. J Chem Phys 2023;158:094902. [PMID: 36889965 DOI: 10.1063/5.0138940] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]  Open
5
Jin J, Voth GA. Statistical Mechanical Design Principles for Coarse-Grained Interactions across Different Conformational Free Energy Surfaces. J Phys Chem Lett 2023;14:1354-1362. [PMID: 36728761 PMCID: PMC9940719 DOI: 10.1021/acs.jpclett.2c03844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
6
Gorai B, Vashisth H. Progress in Simulation Studies of Insulin Structure and Function. Front Endocrinol (Lausanne) 2022;13:908724. [PMID: 35795141 PMCID: PMC9252437 DOI: 10.3389/fendo.2022.908724] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 01/02/2023]  Open
7
Rizzuti B. Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022;1870:140757. [PMID: 35051666 DOI: 10.1016/j.bbapap.2022.140757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/22/2022]
8
Najafi H, Jafari M, Farahavar G, Abolmaali SS, Azarpira N, Borandeh S, Ravanfar R. Recent advances in design and applications of biomimetic self-assembled peptide hydrogels for hard tissue regeneration. Biodes Manuf 2021;4:735-756. [PMID: 34306798 PMCID: PMC8294290 DOI: 10.1007/s42242-021-00149-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/12/2021] [Indexed: 12/22/2022]
9
Schlick T, Portillo-Ledesma S, Myers CG, Beljak L, Chen J, Dakhel S, Darling D, Ghosh S, Hall J, Jan M, Liang E, Saju S, Vohr M, Wu C, Xu Y, Xue E. Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field. Annu Rev Biophys 2021;50:267-301. [PMID: 33606945 PMCID: PMC8105287 DOI: 10.1146/annurev-biophys-091720-102019] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
10
Schlick T, Portillo-Ledesma S. Biomolecular modeling thrives in the age of technology. NATURE COMPUTATIONAL SCIENCE 2021;1:321-331. [PMID: 34423314 PMCID: PMC8378674 DOI: 10.1038/s43588-021-00060-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022]
11
Jin J, Pak AJ, Han Y, Voth GA. A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature. J Chem Phys 2021;154:044105. [PMID: 33514078 PMCID: PMC7826166 DOI: 10.1063/5.0026652] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/14/2020] [Indexed: 11/14/2022]  Open
12
Badu S, Melnik R, Singh S. Mathematical and computational models of RNA nanoclusters and their applications in data-driven environments. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1804564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
13
Seshan G, Kanagasabai S, Ananthasri S, Kannappan B, Suvitha A, Jaimohan SM, Kanagaraj S, Kothandan G. Insights of structure-based pharmacophore studies and inhibitor design against Gal3 receptor through molecular dynamics simulations. J Biomol Struct Dyn 2020;39:6987-6999. [PMID: 32772816 DOI: 10.1080/07391102.2020.1804452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
14
Hinkle KR, Phelan FR. Solvation Free Energy of Self-Assembled Complexes: Using Molecular Dynamics to Understand the Separation of ssDNA-Wrapped Single-Walled Carbon Nanotubes. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2020;124:10.1021/acs.jpcc.0c00983. [PMID: 34136061 PMCID: PMC8204635 DOI: 10.1021/acs.jpcc.0c00983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
15
DeLyser MR, Noid WG. Analysis of local density potentials. J Chem Phys 2019;151:224106. [PMID: 31837690 DOI: 10.1063/1.5128665] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
16
Lebold KM, Noid WG. Dual-potential approach for coarse-grained implicit solvent models with accurate, internally consistent energetics and predictive transferability. J Chem Phys 2019;151:164113. [PMID: 31675902 DOI: 10.1063/1.5125246] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
17
Jin J, Pak AJ, Voth GA. Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability. J Phys Chem Lett 2019;10:4549-4557. [PMID: 31319036 PMCID: PMC6782054 DOI: 10.1021/acs.jpclett.9b01228] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
18
Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019;119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 435] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
19
Atomistic molecular dynamics simulations of the LCST conformational transition in poly(N-vinylcaprolactam) in water. J Mol Graph Model 2019;90:51-58. [PMID: 31009934 DOI: 10.1016/j.jmgm.2019.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/06/2019] [Accepted: 04/09/2019] [Indexed: 11/22/2022]
20
Bansal R, Care A, Lord MS, Walsh TR, Sunna A. Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides. N Biotechnol 2019;52:9-18. [PMID: 30954671 DOI: 10.1016/j.nbt.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/31/2019] [Accepted: 04/01/2019] [Indexed: 12/19/2022]
21
Sharp ME, Vázquez FX, Wagner JW, Dannenhoffer-Lafage T, Voth GA. Multiconfigurational Coarse-Grained Molecular Dynamics. J Chem Theory Comput 2019;15:3306-3315. [PMID: 30897328 PMCID: PMC6660024 DOI: 10.1021/acs.jctc.8b01133] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
22
Pahal V. Quercetin, a secondary metabolite present in methanolic extract of Calendula officinalis, is a potent inhibitor of peptide deformylase, undecaprenyl pyrophosphate synthase and DNA primase enzymes of Staphylococcus aureus: an in vitro and in silico result analysis. ACTA ACUST UNITED AC 2018. [DOI: 10.15406/mojddt.2018.02.00050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
23
Yuan X, Xu Y. Recent Trends and Applications of Molecular Modeling in GPCR⁻Ligand Recognition and Structure-Based Drug Design. Int J Mol Sci 2018;19:ijms19072105. [PMID: 30036949 PMCID: PMC6073596 DOI: 10.3390/ijms19072105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 01/14/2023]  Open
24
Gupta A, Chaudhary N, Aparoy P. MM-PBSA and per-residue decomposition energy studies on 7-Phenyl-imidazoquinolin-4(5H)-one derivatives: Identification of crucial site points at microsomal prostaglandin E synthase-1 (mPGES-1) active site. Int J Biol Macromol 2018;119:352-359. [PMID: 30031079 DOI: 10.1016/j.ijbiomac.2018.07.050] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/29/2022]
25
Schlick T. Adventures with RNA graphs. Methods 2018;143:16-33. [PMID: 29621619 PMCID: PMC6051918 DOI: 10.1016/j.ymeth.2018.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/07/2018] [Accepted: 03/26/2018] [Indexed: 12/20/2022]  Open
26
Bacci M, Langini C, Vymětal J, Caflisch A, Vitalis A. Focused conformational sampling in proteins. J Chem Phys 2018;147:195102. [PMID: 29166086 DOI: 10.1063/1.4996879] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]  Open
27
Thurston BA, Ferguson AL. Machine learning and molecular design of self-assembling -conjugated oligopeptides. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1469754] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
28
Rungsung I, Ramaswamy A. Effects of Peutz-Jeghers syndrome (PJS) causing missense mutations L67P, L182P, G242V and R297S on the structural dynamics of LKB1 (Liver kinase B1) protein. J Biomol Struct Dyn 2018;37:796-810. [PMID: 29447078 DOI: 10.1080/07391102.2018.1441070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
29
Protein Folding in Vivo: From Anfinsen Back to Levinthal. UNDERSTANDING COMPLEX SYSTEMS 2018. [DOI: 10.1007/978-3-319-72218-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
30
Orsi M. Molecular simulation of self-assembly. SELF-ASSEMBLING BIOMATERIALS 2018:305-318. [DOI: 10.1016/b978-0-08-102015-9.00016-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
31
Onufriev AV, Izadi S. Water models for biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1347] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
32
Ramezanghorbani F, Dalgicdir C, Sayar M. A multi-state coarse grained modeling approach for an intrinsically disordered peptide. J Chem Phys 2017;147:094103. [DOI: 10.1063/1.5001087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
33
Bope CD, Tong D, Li X, Lu L. Fluctuation matching approach for elastic network model and structure-based model of biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017;128:100-112. [DOI: 10.1016/j.pbiomolbio.2016.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/25/2016] [Accepted: 12/19/2016] [Indexed: 10/24/2022]
34
HÖft TA, Alpert BK. FAST UPDATING MULTIPOLE COULOMBIC POTENTIAL CALCULATION. SIAM JOURNAL ON SCIENTIFIC COMPUTING : A PUBLICATION OF THE SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS 2017;39:https://doi.org/10.1137/16M1096189. [PMID: 33088167 PMCID: PMC7574401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
35
Rudzinski JF, Lu K, Milner ST, Maranas JK, Noid WG. Extended Ensemble Approach to Transferable Potentials for Low-Resolution Coarse-Grained Models of Ionomers. J Chem Theory Comput 2017;13:2185-2201. [DOI: 10.1021/acs.jctc.6b01160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
36
Effect of solvent model when probing protein dynamics with molecular dynamics. J Mol Graph Model 2017;71:80-87. [DOI: 10.1016/j.jmgm.2016.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
37
Tang Z, Roberts CC, Chang CEA. Understanding ligand-receptor non-covalent binding kinetics using molecular modeling. FRONT BIOSCI-LANDMRK 2017;22:960-981. [PMID: 27814657 PMCID: PMC5470370 DOI: 10.2741/4527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
38
Rychkov GN, Ilatovskiy AV, Nazarov IB, Shvetsov AV, Lebedev DV, Konev AY, Isaev-Ivanov VV, Onufriev AV. Partially Assembled Nucleosome Structures at Atomic Detail. Biophys J 2016;112:460-472. [PMID: 28038734 DOI: 10.1016/j.bpj.2016.10.041] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/06/2016] [Accepted: 10/28/2016] [Indexed: 11/29/2022]  Open
39
Yamamoto S, Nakazawa S, Sugisaki K, Maekawa K, Sato K, Toyota K, Shiomi D, Takui T. Structural Determination of a DNA Oligomer for a Molecular Spin Qubit Lloyd Model of Quantum Computers. Z PHYS CHEM 2016. [DOI: 10.1515/zpch-2016-0799] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
40
Izadi S, Onufriev AV. Accuracy limit of rigid 3-point water models. J Chem Phys 2016;145:074501. [PMID: 27544113 PMCID: PMC4991989 DOI: 10.1063/1.4960175] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/19/2016] [Indexed: 11/14/2022]  Open
41
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5. J Comput Aided Mol Des 2016;30:969-976. [PMID: 27460060 PMCID: PMC5206257 DOI: 10.1007/s10822-016-9926-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/16/2016] [Indexed: 12/14/2022]
42
Perišić O, Schlick T. Computational strategies to address chromatin structure problems. Phys Biol 2016;13:035006. [DOI: 10.1088/1478-3975/13/3/035006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
43
Kim T, Freudenthal BD, Beard WA, Wilson SH, Schlick T. Insertion of oxidized nucleotide triggers rapid DNA polymerase opening. Nucleic Acids Res 2016;44:4409-24. [PMID: 27034465 PMCID: PMC4872097 DOI: 10.1093/nar/gkw174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/04/2016] [Indexed: 11/21/2022]  Open
44
Rodrigues JPGLM, Melquiond ASJ, Bonvin AMJJ. Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016;44:160-167. [PMID: 26751257 DOI: 10.1002/bmb.20941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
45
Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations. MONATSHEFTE FUR CHEMIE 2016;147:553-563. [PMID: 27069282 PMCID: PMC4785218 DOI: 10.1007/s00706-016-1674-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/14/2016] [Indexed: 01/23/2023]
46
Anandakrishnan R, Drozdetski A, Walker RC, Onufriev AV. Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J 2016;108:1153-64. [PMID: 25762327 DOI: 10.1016/j.bpj.2014.12.047] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 12/23/2014] [Accepted: 12/29/2014] [Indexed: 11/24/2022]  Open
47
Dunn NJH, Noid WG. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids. J Chem Phys 2015;143:243148. [DOI: 10.1063/1.4937383] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
48
Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic Acids Res 2015;44:e63. [PMID: 26687716 PMCID: PMC4838351 DOI: 10.1093/nar/gkv1479] [Citation(s) in RCA: 236] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/05/2015] [Indexed: 01/08/2023]  Open
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Ozer G, Luque A, Schlick T. The chromatin fiber: multiscale problems and approaches. Curr Opin Struct Biol 2015;31:124-39. [PMID: 26057099 DOI: 10.1016/j.sbi.2015.04.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 12/20/2022]
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Chandramouli B, Zazza C, Mancini G, Brancato G. Boundary condition effects on the dynamic and electric properties of hydration layers. J Phys Chem A 2015;119:5465-75. [PMID: 25752804 DOI: 10.1021/jp511824t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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