onr:"swepub:oai:lup.lub.lu.se:5663cbf3-f18c-4429-b4ec-1d0169d9cb1f"
Search: onr:"swepub:oai:lup.lub.lu.se:5663cbf3-f18c-4429-b4ec-1d0169d9cb1f" > A comparison of dif...
- 1 of 1
- Previous record
- Next record
- To hitlist
- Genheden, SamuelLund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH (author)
A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations.
- Article/chapterEnglish2011
Publisher, publication year, extent ...
- 2010-12-06
- Wiley,2011
- electronicrdacarrier
Numbers
- LIBRIS-ID:oai:lup.lub.lu.se:5663cbf3-f18c-4429-b4ec-1d0169d9cb1f
- https://lup.lub.lu.se/record/1756716URI
- https://doi.org/10.1002/jcc.21546DOI
Supplementary language notes
- Language:English
- Summary in:English
Part of subdatabase
- SwePubSwePub
Classification
Notes
- We study how the results of molecular dynamics (MD) simulations are affected by various choices during the setup, e.g., the starting velocities, the solvation, the location of protons, the conformation of His, Asn, and Gln residues, the protonation and titration of His residues, and the treatment of alternative conformations. We estimate the binding affinity of ligands to four proteins calculated with the MM/GBSA method (molecular mechanics combined with a generalized Born and surface area solvation energy). For avidin and T4 lysozyme, all variations gave similar results within 2 kJ/mol. For factor Xa, differences in the solvation or in the selection of alternative conformations gave results that are significantly different from those of the other approaches by 4-6 kJ/mol, whereas for galectin-3, changes in the conformations, rotations, and protonation gave results that differed by 10 kJ/mol, but only if residues close to the binding site were modified. This shows that the results of MM/GBSA calculations are reasonably reproducible even if the MD simulations are set up with different software. Moreover, we show that the sampling of phase space can be enhanced by solvating the systems with different equilibrated water boxes, in addition to the common use of different starting velocities. If different conformations are available in the crystal structure, they should also be employed to enhance the sampling. Protonation, ionization, and conformations of Asn, Gln, and His may also be used to enhance sampling, but great effort should be spent to obtain as reliable predictions as possible close to the active site.
Subject headings and genre
Added entries (persons, corporate bodies, meetings, titles ...)
- Ryde, UlfLund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH(Swepub:lu)teok-ury (author)
- BeräkningskemiEnheten för fysikalisk och teoretisk kemi (creator_code:org_t)
Related titles
- In:Journal of Computational Chemistry: Wiley32:2, s. 187-1951096-987X0192-8651
Internet link
Find in a library
- Journal of Computational Chemistry (Search for host publication in LIBRIS)
To the university's database
- 1 of 1
- Previous record
- Next record
- To hitlist
Find more in SwePub
- By the author/editor
- Genheden, Samuel
- Ryde, Ulf
- About the subject
-
- NATURAL SCIENCES
- NATURAL SCIENCES
- and Chemical Science ...
- and Theoretical Chem ...
- Articles in the publication
- Journal of Compu ...
- By the university
- Lund University
Search outside SwePub
- Extend your search to:
- Google Book Search
- Google Scholar
Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.
- Copyright © LIBRIS - National Library Systems
- LIBRIS.kb.se
