Suppr超能文献

Collective variable approaches for single molecule flexible fitting and enhanced sampling.

作者信息

Vashisth Harish, Skiniotis Georgios, Brooks Charles Lee

机构信息

Department of Chemical Engineering, University of New Hampshire , Durham, New Hampshire 03824, United States.

出版信息

Chem Rev. 2014 Mar 26;114(6):3353-65. doi: 10.1021/cr4005988. Epub 2014 Jan 21.

Abstract
摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0670/3983124/323bd10bd426/cr-2013-005988_0005.jpg

相似文献

1
Collective variable approaches for single molecule flexible fitting and enhanced sampling.
Chem Rev. 2014 Mar 26;114(6):3353-65. doi: 10.1021/cr4005988. Epub 2014 Jan 21.
2
A quantitative model of thermal stabilization and destabilization of proteins by ligands.
Biophys J. 2008 Oct;95(7):3222-31. doi: 10.1529/biophysj.108.134973. Epub 2008 Jul 3.
3
A novel two-site binding equation presented in terms of the total ligand concentration.
FEBS Lett. 1996 Sep 2;392(3):245-9. doi: 10.1016/0014-5793(96)00818-6.
4
Allosteric communication occurs via networks of tertiary and quaternary motions in proteins.
PLoS Comput Biol. 2009 Feb;5(2):e1000293. doi: 10.1371/journal.pcbi.1000293. Epub 2009 Feb 20.
5
Rational design of affinity peptide ligand by flexible docking simulation.
J Chromatogr A. 2007 Mar 30;1146(1):41-50. doi: 10.1016/j.chroma.2007.01.130. Epub 2007 Feb 4.
7
Unraveling the symmetry ambiguity in a hexamer: calculation of the R6 human insulin structure.
J Biomol NMR. 2000 Feb;16(2):93-108. doi: 10.1023/a:1008323819099.
8
Computational approaches to molecular recognition.
Curr Opin Chem Biol. 1997 Dec;1(4):449-57. doi: 10.1016/s1367-5931(97)80038-5.
9
New approaches for computing ligand-receptor binding kinetics.
Curr Opin Struct Biol. 2018 Apr;49:1-10. doi: 10.1016/j.sbi.2017.10.001. Epub 2017 Nov 11.
10
PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.
Acta Crystallogr D Biol Crystallogr. 2004 Aug;60(Pt 8):1355-63. doi: 10.1107/S0907444904011679. Epub 2004 Jul 21.

引用本文的文献

1
Structural and computational studies of HIV-1 RNA.
RNA Biol. 2024 Jan;21(1):1-32. doi: 10.1080/15476286.2023.2289709. Epub 2023 Dec 15.
3
All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors.
Front Endocrinol (Lausanne). 2016 Jun 20;7:68. doi: 10.3389/fendo.2016.00068. eCollection 2016.
4
Theoretical and computational studies of peptides and receptors of the insulin family.
Membranes (Basel). 2015 Feb 11;5(1):48-83. doi: 10.3390/membranes5010048.

本文引用的文献

1
Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data.
J Chem Theory Comput. 2010 Sep 14;6(9):2990-3002. doi: 10.1021/ct100374a. Epub 2010 Aug 23.
3
Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions.
J Chem Theory Comput. 2013 Jun 11;9(6):2849-56. doi: 10.1021/ct400191b. Epub 2013 May 16.
4
From metadynamics to dynamics.
Phys Rev Lett. 2013 Dec 6;111(23):230602. doi: 10.1103/PhysRevLett.111.230602. Epub 2013 Dec 3.
5
Collective variable description of native protein dynamics.
Annu Rev Phys Chem. 1995;46:223-50. doi: 10.1146/annurev.pc.46.100195.001255.
6
Free-energy landscape of protein oligomerization from atomistic simulations.
Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):E4708-13. doi: 10.1073/pnas.1320077110. Epub 2013 Nov 18.
8
iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates.
J Struct Biol. 2013 Nov;184(2):261-70. doi: 10.1016/j.jsb.2013.08.010. Epub 2013 Aug 30.
9
Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality.
J Chem Theory Comput. 2013 Aug 13;9(8):3843-3847. doi: 10.1021/ct400260c. Epub 2013 Jul 3.
10
Comparative study of selected parallel tempering methods.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jul;88(1):013312. doi: 10.1103/PhysRevE.88.013312. Epub 2013 Jul 30.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验