Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors.

Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors. Abstract Text:

Since the evaluation of ligand conformations is a crucial aspect of structure-based virtual screening, scoring functions play significant roles in it. However, it is known that a scoring function does not always work well for all target proteins. When one cannot know which scoring function works best against a target protein a priori, there is no standard scoring method to know it even if 3D structure of a target protein-ligand complex is available. Therefore, development of the method to achieve high enrichments from given scoring functions and 3D structure of protein-ligand complex is a crucial and challenging task. To address this problem, we applied SCS (supervised consensus scoring), which employs a rough linear correlation between the binding free energy and the root-mean-square deviation (rmsd) of a native ligand conformations and incorporates protein-ligand binding process with docked ligand conformations using supervised learning, to virtual screening. We evaluated both the docking poses and enrichments of SCS and five scoring functions (F-Score, G-Score, D-Score, ChemScore, and PMF) for three different target proteins: thymidine kinase (TK), thrombin (thrombin), and peroxisome proliferator-activated receptor gamma (PPARgamma). Our enrichment studies show that SCS is competitive or superior to a best single scoring function at the top ranks of screened database. We found that the enrichments of SCS could be limited by a best scoring function, because SCS is obtained on the basis of the five individual scoring functions. Therefore, it is concluded that SCS works very successfully from our results. Moreover, from docking pose analysis, we revealed the connection between enrichment and average centroid distance of top-scored docking poses. Since SCS requires only one 3D structure of protein-ligand complex, SCS will be useful for identifying new ligands.

Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors. Publishing Authors By Initials

For similar abstracts research abstracts see: abstracts research

PUBMED ID PMID:

MEDLINE DATE:

Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Journal of chemical information and modeling

VOLUME: 48

Page Numbers: 747-54

Journal Abbreviation:

ISSN: 1549-9596

DAY: 5

MONTH: 03

YEAR: 2008

Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 101230060

Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors. Keywords Mesh Terms:

KEYWORDS:

MESH TERMS:

Chemical & Substance for Abstract: Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors. Information

Substance Name:

Registry Number:

Grant and Affiliation Information for Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors.

AFFILIATION: Bio-IT Center and Nano Electronics Research Laboratories, NEC Corporation, 34, Miyukigaoka, Tsukuba, Ibaraki 305-8501, Japan r-teramoto@bq.jp.nec.com.

Country: United States

AGENCY:

GRANT:

ACRONYM:

MEDLINETA: J Chem Inf Model

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors Related Publications

• Choriocarcinomatous change with immunocytochemically HCG-positive cells in the gastric carcinoma of the males.
• Consensus scoring with feature selection for structure-based virtual screening.
• Dendrite classification in rat hippocampal neurons according to signal propagation properties. Observation by multichannel optical recording in cultured neuronal networks.
• Non-invasive thymoma with widespread blood-borne metastasis.
• Serum alpha-fetoprotein-positive gastric carcinoid with liver metastasis.
• Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors.
• Tracking guide for optical disks formed by photodarkening as As-Se-S-Ge amorphous film.