ArticleScientific reports2012
How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases.
Article in Scientific reports, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.Nature communications · 2024Article
- Identification of Novel Protein Targets of Prodigiosin for Breast Cancer Using Inverse Virtual Screening Methods.Applied biochemistry and biotechnology · 2023Article
- Mapping roles of active site residues in the acceptor site of the PA3944 Gcn5-related N-acetyltransferase enzyme.Protein science : a publication of the Protein Society · 2023Article
- Article
- Highly potent natural fungicides identified in silico against the cereal killer fungus Magnaporthe oryzae.Scientific reports · 2022Article
- In Silico Study to Identify New Antituberculosis Molecules from Natural Sources by Hierarchical Virtual Screening and Molecular Dynamics Simulations.Pharmaceuticals (Basel, Switzerland) · 2019Article
- Insight into the interaction mechanism of human SGLT2 with its inhibitors: 3D-QSAR studies, homology modeling, and molecular docking and molecular dynamics simulations.Journal of molecular modeling · 2018Article
- Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae.BMC systems biology · 2015Article
- An approach for catalyst design in artificial photosynthetic systems: focus on nanosized inorganic cores within proteins.Photosynthesis research · 2013Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular docking is the most commonly used technique in the modern drug discovery process where computational approaches involving docking algorithms are used to dock small molecules into macromolecular target structures. Over the recent years several evaluation studies have been reported by independent scientists comparing the performance of the docking programs by using default 'black box' protocols supplied by the software companies. Such studies have to be considered carefully as the docking programs can be tweaked towards optimum performance by selecting the parameters suitable for the target of interest. In this study we address the problem of selecting an appropriate docking and scoring function combination (88 docking algorithm-scoring functions) for substrate specificity predictions for feruloyl esterases, an industrially relevant enzyme family. We also propose the 'Key Interaction Score System' (KISS), a more biochemically meaningful measure for evaluation of docking programs based on pose prediction accuracy.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.