A continuum solvent model: the DISOLV program - algorithms, implementation, and validation
Numerical Methods and Programming, V.12, P.246-261 (2011) Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the DISOL...
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| creator | Kupervasser, Oleg Zhabin, S. N Martynov, Ya. B Fedulov, K. M Oferkin, I. F Sulimov, A. V Sulimov, V. B |
| description | Numerical Methods and Programming, V.12, P.246-261 (2011) Several implicit (continuum) solvent models are considered: the Polarized
Continuum Model (PCM), the Surface Generalized Born model (SGB), and the
COnductor-like Screening model (COSMO) as well as their implementation in the
form of the DISOLV program. The methods for solving the corresponding equations
and for computing the analytic gradients are described. The analytic gradients
are used for the fast local energy optimization of molecules in a solvent. An
algorithm for the original smooth triangulated molecular surface construction
is shortly discussed. The procedure for matching the model parameters and the
results of the program application to proteins and ligands with the employment
of the MMFF94 force field are described. The validation results show the
capability of the program to reach a good accuracy (about several tenth of
kcal/mol) in the case of the solvation energy calculation for reasonable time
periods at arbitrary shifts of the triangulated grid in use for such large
molecules as proteins. A good agreement between the calculated and
experimentally measured solvation energies in water is obtained with a
root-mean-square deviation about 0.8 kcal/mol for several hundreds of
molecules. |
| doi_str_mv | 10.48550/arxiv.1107.0404 |
| format | Article |
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Continuum Model (PCM), the Surface Generalized Born model (SGB), and the
COnductor-like Screening model (COSMO) as well as their implementation in the
form of the DISOLV program. The methods for solving the corresponding equations
and for computing the analytic gradients are described. The analytic gradients
are used for the fast local energy optimization of molecules in a solvent. An
algorithm for the original smooth triangulated molecular surface construction
is shortly discussed. The procedure for matching the model parameters and the
results of the program application to proteins and ligands with the employment
of the MMFF94 force field are described. The validation results show the
capability of the program to reach a good accuracy (about several tenth of
kcal/mol) in the case of the solvation energy calculation for reasonable time
periods at arbitrary shifts of the triangulated grid in use for such large
molecules as proteins. A good agreement between the calculated and
experimentally measured solvation energies in water is obtained with a
root-mean-square deviation about 0.8 kcal/mol for several hundreds of
molecules.</description><identifier>DOI: 10.48550/arxiv.1107.0404</identifier><language>eng</language><subject>Physics - Chemical Physics</subject><creationdate>2011-07</creationdate><rights>http://arxiv.org/licenses/nonexclusive-distrib/1.0</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>228,230,781,886</link.rule.ids><linktorsrc>$$Uhttps://arxiv.org/abs/1107.0404$$EView_record_in_Cornell_University$$FView_record_in_$$GCornell_University$$Hfree_for_read</linktorsrc><backlink>$$Uhttps://doi.org/10.48550/arXiv.1107.0404$$DView paper in arXiv$$Hfree_for_read</backlink></links><search><creatorcontrib>Kupervasser, Oleg</creatorcontrib><creatorcontrib>Zhabin, S. N</creatorcontrib><creatorcontrib>Martynov, Ya. B</creatorcontrib><creatorcontrib>Fedulov, K. M</creatorcontrib><creatorcontrib>Oferkin, I. F</creatorcontrib><creatorcontrib>Sulimov, A. V</creatorcontrib><creatorcontrib>Sulimov, V. B</creatorcontrib><title>A continuum solvent model: the DISOLV program - algorithms, implementation, and validation</title><description>Numerical Methods and Programming, V.12, P.246-261 (2011) Several implicit (continuum) solvent models are considered: the Polarized
Continuum Model (PCM), the Surface Generalized Born model (SGB), and the
COnductor-like Screening model (COSMO) as well as their implementation in the
form of the DISOLV program. The methods for solving the corresponding equations
and for computing the analytic gradients are described. The analytic gradients
are used for the fast local energy optimization of molecules in a solvent. An
algorithm for the original smooth triangulated molecular surface construction
is shortly discussed. The procedure for matching the model parameters and the
results of the program application to proteins and ligands with the employment
of the MMFF94 force field are described. The validation results show the
capability of the program to reach a good accuracy (about several tenth of
kcal/mol) in the case of the solvation energy calculation for reasonable time
periods at arbitrary shifts of the triangulated grid in use for such large
molecules as proteins. A good agreement between the calculated and
experimentally measured solvation energies in water is obtained with a
root-mean-square deviation about 0.8 kcal/mol for several hundreds of
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Continuum Model (PCM), the Surface Generalized Born model (SGB), and the
COnductor-like Screening model (COSMO) as well as their implementation in the
form of the DISOLV program. The methods for solving the corresponding equations
and for computing the analytic gradients are described. The analytic gradients
are used for the fast local energy optimization of molecules in a solvent. An
algorithm for the original smooth triangulated molecular surface construction
is shortly discussed. The procedure for matching the model parameters and the
results of the program application to proteins and ligands with the employment
of the MMFF94 force field are described. The validation results show the
capability of the program to reach a good accuracy (about several tenth of
kcal/mol) in the case of the solvation energy calculation for reasonable time
periods at arbitrary shifts of the triangulated grid in use for such large
molecules as proteins. A good agreement between the calculated and
experimentally measured solvation energies in water is obtained with a
root-mean-square deviation about 0.8 kcal/mol for several hundreds of
molecules.</abstract><doi>10.48550/arxiv.1107.0404</doi><oa>free_for_read</oa></addata></record> |
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| title | A continuum solvent model: the DISOLV program - algorithms, implementation, and validation |
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