| Efficient calculation of molecular properties from simulation using kernel molecular dynamics. | |
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MedLine Citation:
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PMID: 18672870 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Understanding the relationship between chemical structure and function is a ubiquitous problem within the fields of chemistry and biology. Simulation approaches attack the problem utilizing physics to understand a given process at the particle level. Unfortunately, these approaches are often too expensive for many problems of interest. Informatics approaches attack the problem with empirical analysis of descriptions of chemical structure. The issue in these methods is how to describe molecules in a manner that facilitates accurate and general calculation of molecular properties. Here, we present a novel approach that utilizes aspects of simulation and informatics in order to formulate structure-property relationships. We show how supervised learning can be utilized to overcome the sampling problem in simulation approaches. Likewise, we show how learning can be achieved based on molecular descriptions that are rooted in the physics of dynamic intermolecular forces. We apply the approach to three problems including the analysis of corticosteroid binding globulin ligand binding affinity, identification of formylpeptide receptor ligands, and identification of resveratrol analogues capable of inhibiting activation of transcription factor nuclear factor kappaB. |
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Authors:
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W Michael Brown; Ariella Sasson; Donald R Bellew; Lucy A Hunsaker; Shawn Martin; Andrei Leitao; Lorraine M Deck; David L Vander Jagt; Tudor I Oprea |
Publication Detail:
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Type: Journal Article; Research Support, U.S. Gov't, Non-P.H.S. Date: 2008-08-02 |
Journal Detail:
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Title: Journal of chemical information and modeling Volume: 48 ISSN: 1549-9596 ISO Abbreviation: - Publication Date: 2008 Aug |
Date Detail:
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Created Date: 2008-08-26 Completed Date: 2008-10-03 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101230060 Medline TA: J Chem Inf Model Country: United States |
Other Details:
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Languages: eng Pagination: 1626-37 Citation Subset: IM |
Affiliation:
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Computational Biology, Sandia National Laboratories, Albuquerque, New Mexico 87185-1316, USA. wmbrown@sandia.gov |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Computer Simulation* Globulins / chemistry, metabolism Ligands Models, Molecular Molecular Conformation NF-kappa B / chemistry, metabolism Steroids / chemistry, metabolism Stilbenes / chemistry, metabolism |
| Chemical | |
Reg. No./Substance:
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0/Globulins; 0/Ligands; 0/NF-kappa B; 0/Steroids; 0/Stilbenes |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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