ArticleJournal of computational chemistry2011
Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons.
Article in Journal of computational chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 64 citations in OpenAlex.
- 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
- Mutations in Mig6 reduce inhibition of the epidermal growth factor receptor.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2024Article
- Considerations Around Structure-Based Drug Discovery for KRAS Using DOCK.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Neutral ceramidase-active site inhibitor chemotypes and binding modes.Bioorganic chemistry · 2023Article
- Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit.Journal of chemical information and modeling · 2023Article
- Discovery and molecular basis of subtype-selective cyclophilin inhibitors.Nature chemical biology · 2022Article
- Validation of an Allosteric Binding Site of Src Kinase Identified by Unbiased Ligand Binding Simulations.Journal of molecular biology · 2022Article
- fingeRNAt-A novel tool for high-throughput analysis of nucleic acid-ligand interactions.PLoS computational biology · 2022Article
- Identification of Zika Virus Inhibitors Using Homology Modeling and Similarity-Based Screening to Target Glycoprotein E.Biochemistry · 2020Article
- Assessing Molecular Docking Tools to Guide Targeted Drug Discovery of CD38 Inhibitors.International journal of molecular sciences · 2020Article
- Dimethylaminophenyl Hydrazides as Inhibitors of the Lipid Transport Protein LprG in Mycobacteria.ACS infectious diseases · 2020Article
- Identification of Fatty Acid Binding Protein 5 Inhibitors Through Similarity-Based Screening.Biochemistry · 2019Article
- Assessing and improving the performance of consensus docking strategies using the DockBox package.Journal of computer-aided molecular design · 2019Article
- Identification of Ebola Virus Inhibitors Targeting GP2 Using Principles of Molecular Mimicry.Journal of virology · 2019Article
- Identification of a Water-Coordinating HER2 Inhibitor by Virtual Screening Using Similarity-Based Scoring.Biochemistry · 2018Article
- ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research.Journal of chemical information and modeling · 2017Article
- Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets.Journal of computational chemistry · 2017Article
- Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-heptad repeat trimer.Bioorganic & medicinal chemistry letters · 2017Article
- The Antinociceptive Agent SBFI-26 Binds to Anandamide Transporters FABP5 and FABP7 at Two Different Sites.Biochemistry · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A docking-rescoring method, based on per-residue van der Waals (VDW), electrostatic (ES), or hydrogen bond (HB) energies has been developed to aid discovery of ligands that have interaction signatures with a target (footprints) similar to that of a reference. Biologically useful references could include known drugs, inhibitors, substrates, transition states, or side-chains that mediate protein-protein interactions. Termed footprint similarity (FPS) score, the method, as implemented in the program DOCK, was validated and characterized using: (1) pose identification, (2) crossdocking, (3) enrichment, and (4) virtual screening. Improvements in pose identification (6–12%) were obtained using footprint-based (FPS(VDW+ES)) vs. standard DOCK (DCE(VDW+ES)) scoring as evaluated on three large datasets (680–775 systems) from the SB2010 database. Enhanced pose identification was also observed using FPS (45.4% or 70.9%) compared with DCE (17.8%) methods to rank challenging crossdocking ensembles from carbonic anhydrase. Enrichment tests, for three representative systems, revealed FPSVDW+ES scoring yields significant early fold enrichment in the top 10% of ranked databases. For EGFR, top FPS poses are nicely accommodated in the molecular envelope defined by the reference in comparison with DCE, which yields distinct molecular weight bias toward larger molecules. Results from a representative virtual screen of ca. 1 million compounds additionally illustrate how ligands with footprints similar to a known inhibitor can readily be identified from within large commercially available databases. By providing an alternative way to rank ligand poses in a simple yet directed manner we anticipate that FPS scoring will be a useful tool for docking and structure-based design.
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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.