ArticleThe journal of physical chemistry. B2015
Pharmacophore-based similarity scoring for DOCK.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- DOCKweb: a web-based GUI platform for molecular modeling with DOCK6.Journal of computer-aided molecular design · 2026Article
- Fragment and torsion biasing algorithms for construction of small organic molecules in proteins using DOCK.Journal of computational chemistry · 2025Article
- Consensus screening for a challenging target: the quest for P-glycoprotein inhibitors.RSC medicinal chemistry · 2024Article
- A molecular evolution algorithm for ligand design in DOCK.Journal of computational chemistry · 2022Article
- Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery.Molecular systems biology · 2022Article
- Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions.Journal of chemical information and modeling · 2022Review
- Leveraging nonstructural data to predict structures and affinities of protein-ligand complexes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- DockingApp RF: A State-of-the-Art Novel Scoring Function for Molecular Docking in a User-Friendly Interface to AutoDock Vina.International journal of molecular sciences · 2020Article
- Identification of Zika Virus Inhibitors Using Homology Modeling and Similarity-Based Screening to Target Glycoprotein E.Biochemistry · 2020Article
- A computational strategy to understand structure-activity relationship of 1,3-disubstituted imidazole [1,5-α] pyrazine derivatives described as ATP competitive inhibitors of the IGF-1 receptor related to Ewing sarcoma.Journal of molecular modeling · 2020Article
- Application of MM-PBSA Methods in Virtual Screening.Molecules (Basel, Switzerland) · 2020Review
- Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions.Journal of chemical information and modeling · 2019Article
- Identification of Fatty Acid Binding Protein 5 Inhibitors Through Similarity-Based Screening.Biochemistry · 2019Article
- Molecular Docking: Shifting Paradigms in Drug Discovery.International journal of molecular sciences · 2019Review
- DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state.Journal of cheminformatics · 2019Article
- Identification of Ebola Virus Inhibitors Targeting GP2 Using Principles of Molecular Mimicry.Journal of virology · 2019Article
- Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses.Molecules (Basel, Switzerland) · 2019Article
- Pharmacophore modeling, docking and molecular dynamics to identify Leishmania major farnesyl pyrophosphate synthase inhibitors.Journal of molecular modeling · 2018Article
- Virtual screening to identify Leishmania braziliensis N-myristoyltransferase inhibitors: pharmacophore models, docking, and molecular dynamics.Journal of molecular modeling · 2018Article
- Identification of a Water-Coordinating HER2 Inhibitor by Virtual Screening Using Similarity-Based Scoring.Biochemistry · 2018Article
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Authors and funding
2 authors.
Funding
Abstract
Pharmacophore modeling incorporates geometric and chemical features of known inhibitors and/or targeted binding sites to rationally identify and design new drug leads. In this study, we have encoded a three-dimensional pharmacophore matching similarity (FMS) scoring function into the structure-based design program DOCK. Validation and characterization of the method are presented through pose reproduction, crossdocking, and enrichment studies. When used alone, FMS scoring dramatically improves pose reproduction success to 93.5% (∼20% increase) and reduces sampling failures to 3.7% (∼6% drop) compared to the standard energy score (SGE) across 1043 protein-ligand complexes. The combined FMS+SGE function further improves success to 98.3%. Crossdocking experiments using FMS and FMS+SGE scoring, for six diverse protein families, similarly showed improvements in success, provided proper pharmacophore references are employed. For enrichment, incorporating pharmacophores during sampling and scoring, in most cases, also yield improved outcomes when docking and rank-ordering libraries of known actives and decoys to 15 systems. Retrospective analyses of virtual screenings to three clinical drug targets (EGFR, IGF-1R, and HIVgp41) using X-ray structures of known inhibitors as pharmacophore references are also reported, including a customized FMS scoring protocol to bias on selected regions in the reference. Overall, the results and fundamental insights gained from this study should benefit the docking community in general, particularly researchers using the new FMS method to guide computational drug discovery with DOCK.
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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.