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molecular dynamics

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Book Chapter
Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_005
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
...Huang, Y., “Simulating membrane proteins with constant pH molecular dynamics,” in A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules, edited by Y. Wang and R. Zhou (AIP Publishing, Melville, New York, 2023), pp. 5-1–5-14. Introduction pH represents...
Book Chapter
Series: AIPP Books, Methods
Published: August 2021
10.1063/9780735422377_004
EISBN: 978-0-7354-2237-7
ISBN: 978-0-7354-2234-6
...Tee, S. R. (2021), “Theory and practice in constant potential molecular dynamics simulations,” in Wang, Y. (ed.), Multiscale Modeling of Electrochemical Reactions and Processes, Melville, New York: AIP Publishing, pp. 4-1–4-18. molecular dynamics computational physics thermodynamics...
Images
(a) Schematic representation of conformational transition from state A (“Op...
Published: January 2023
FIG. 9.1 (a) Schematic representation of conformational transition from state A (“Open”) to state B (“Close”) for protein functional dynamics; (b) A normal system set for all-atom molecular dynamics simulation that contains biomolecules, water, metal ions, and so on; (c) The evolution of a path to... More about this image found in (a) Schematic representation of conformational transition from state A (“Op...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
...References References Allen , W. , Lemkul , J. , and Bevan , D. , “ Gridmat-Md: A grid-based membrane analysis tool for use with molecular dynamics ,” J. Comput. Chem.   30 , 1952 – 1958 ( 2009 ). 10.1002/jcc.21172 Anandakrishnan , R. , Aguilar , B...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... Doerr , S. , Harvey , M. J. , Noe , F. , and De Fabritiis , G. , “ HTMD: High-throughput molecular dynamics for molecular discovery ,” J. Chem. Theory Comput.   12 ( 4 ), 1845 – 1852 ( 2016 ). 10.1021/acs.jctc.6b00049 Ester , M. , Kriegel , H.-P. , Sander , J...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... Eastman , P. , Swails , J. , Chodera , J. D. , McGibbon , R. T. , Zhao , Y. , Beauchamp , K. A.   , “ OpenMM 7: Rapid development of high performance algorithms for molecular dynamics ,” PLoS Comput. Biol.   13 ( 7 ), e1005659 ( 2017 ). 10.1371/journal.pcbi.1005659...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
...-Metric logP 10. Determination of liposomal membrane-water partition coefficients of lonizable drugs ,” Pharm. Res.   15 ( 2 ), 209 – 215 ( 1998 ). 10.1023/A:1011954332221 Baptista , A. M. , Teixeira , V. H. , and Soares , C. M. , “ Constant-pH molecular dynamics using stochastic...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
.... , and Selloni , A. , “ Free energy of proton transfer at the water–TiO2 interface from ab initio deep potential molecular dynamics ,” Chem. Sci.   11 , 2335 – 2341 ( 2020 ). 10.1039/C9SC05116C Case , D. A. , Belfon , K. , Ben-Shalom , I. Y. , Brozell , S. R. , Cerutti...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
.... R. , and Schulten , K. , “ Enhanced sampling techniques in molecular dynamics simulations of biological systems ,” Biochim. Biophys. Acta Gen. Subj.   1850 ( 5 ), 872 – 877 ( 2015 ). 10.1016/j.bbagen.2014.10.019 Bolhuis , P. G. , Dellago , C. , and Chandler , D...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... performance algorithms for molecular dynamics ,” PLOS Comput. Biol.   13 , e1005659 ( 2017 ). 10.1371/journal.pcbi.1005659 Empereur-Mot , C. , Pesce , L. , Doni , G. , Bochicchio , D. , Capelli , R. , Perego , C. , and Pavan , G. M. , “ Swarm-CG: Automatic...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
.... , and Pantano , S. , “ Fat SIRAH: Coarse-grained phospholipids to explore membrane–protein dynamics ,” J. Chem. Theory Comput.   15 , 5674 – 5688 ( 2019 ). 10.1021/acs.jctc.9b00435 Chavent , M. , Duncan , A. L. , and Sansom , M. S. P. , “ Molecular dynamics simulations of membrane...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_010
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... ), these structures only capture a static metastable state of the biomolecule and provide limited information on the dynamics of functional conformational changes ( Karplus and Kuriyan, 2005 ). Although other experimental methods, such as nuclear magnetic resonance spectroscopy and single-molecular fluorescence...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
.../PhysRevLett.100.020603 Berendsen , H. J. , Postma , J. V. , van Gunsteren , W. F. , DiNola , A. R. H. J. , and Haak , J. R. , “ Molecular dynamics with coupling to an external bath ,” J. Chem. Phys.   81 , 3684 – 3690 ( 1984 ). 10.1063/1.448118 Best , R. B...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_006
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
..., 2023), pp. 6-1–6-20. Introduction Over the last few decades, molecular dynamics (MD) simulations have attracted a great deal of attention due to their wide range of applications in many fields such as condensed matter physics, materials science, polymer chemistry, and molecular biology. They provide...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_003
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... and Nicolson, 1972 ) to a highly complex and tightly regulated hub of interactions and signaling processes ( Goñi, 2014 ). In parallel, advances in molecular dynamics (MD) simulations nowadays provide a perspective on the structure and dynamics of membrane systems that is difficult to achieve using...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_004
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
.... , Teixeira , V. H. , and Soares , C. M. , “ Constant-pH molecular dynamics using stochastic titration ,” J. Chem. Phys.   117 ( 9 ), 4184 – 4200 ( 2002 ). 10.1063/1.1497164 Bennett , W. F. D. , Chen , A. W. , Donnini , S. , Groenhof , G. , and Tieleman , D. P...
Book
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_frontmatter
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
...) Machine learning (Interdisciplinary physics) Preface Molecular simulations allow us to see the “invisible” biological world with super high time and spatial resolution. Molecular modeling and molecular dynamics (MD) simulation of biomolecules have increasingly become essential and irreplaceable tools...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_008
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
.... A.   , “ OpenMM 7: Rapid development of high performance algorithms for molecular dynamics ,” PLoS Comput. Biol.   13 ( 7 ), e1005659 ( 2017 ). 10.1371/journal.pcbi.1005659 Ensing , B. , De Vivo , M. , Liu , Z. , Moore , P. , and Klein , M. L. , “ Metadynamics as a tool...
Book Chapter
Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... application for protein preparation for molecular dynamics simulations ,” J. Chem. Inf. Model.   57 , 1511 – 1516 ( 2017 ). 10.1021/acs.jcim.7b00190 Mey , A. S. J. S.   , “ Best practices for alchemical free energy calculations [Article v1.0] ,” Living J. Comput. Mol. Sci.   2,   18378 ( 2020...