ArticleJournal of computational chemistry2013
Grid-based molecular footprint comparison method for docking and de novo design: application to HIVgp41.
Article in Journal of computational chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 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
- Protein-Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions.The journal of physical chemistry. B · 2024Article
- Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit.Journal of chemical information and modeling · 2023Article
- Evaluating Known Zika Virus NS2B-NS3 Protease Inhibitor Scaffolds via In Silico Screening and Biochemical Assays.Pharmaceuticals (Basel, Switzerland) · 2023Article
- A molecular evolution algorithm for ligand design in DOCK.Journal of computational chemistry · 2022Article
- Identification of Zika Virus Inhibitors Using Homology Modeling and Similarity-Based Screening to Target Glycoprotein E.Biochemistry · 2020Article
- Identification of Fatty Acid Binding Protein 5 Inhibitors Through Similarity-Based Screening.Biochemistry · 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
- Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets.Journal of computational chemistry · 2017Article
- The Antinociceptive Agent SBFI-26 Binds to Anandamide Transporters FABP5 and FABP7 at Two Different Sites.Biochemistry · 2017Article
- Small molecule inhibitors of HIVgp41 N-heptad repeat trimer formation.Bioorganic & medicinal chemistry letters · 2015Article
- DOCK 6: Impact of new features and current docking performance.Journal of computational chemistry · 2015Article
- Pharmacophore-based similarity scoring for DOCK.The journal of physical chemistry. B · 2015Article
- Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design.Journal of chemical information and modeling · 2014Article
- Strategies for lead discovery: application of footprint similarity targeting HIVgp41.Bioorganic & medicinal chemistry · 2014Article
- Inhibition of fatty acid binding proteins elevates brain anandamide levels and produces analgesia.PloS one · 2014Article
- Ligand pose and orientational sampling in molecular docking.PloS one · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Scoring functions are a critically important component of computer-aided screening methods for the identification of lead compounds during early stages of drug discovery. Here, we present a new multigrid implementation of the footprint similarity (FPS) scoring function that was recently developed in our laboratory which has proven useful for identification of compounds which bind to a protein on a per-residue basis in a way that resembles a known reference. The grid-based FPS method is much faster than its Cartesian-space counterpart, which makes it computationally tractable for on-the-fly docking, virtual screening, or de novo design. In this work, we establish that: (i) relatively few grids can be used to accurately approximate Cartesian space footprint similarity, (ii) the method yields improved success over the standard DOCK energy function for pose identification across a large test set of experimental co-crystal structures, for crossdocking, and for database enrichment, and (iii) grid-based FPS scoring can be used to tailor construction of new molecules to have specific properties, as demonstrated in a series of test cases targeting the viral protein HIVgp41. The method is available in the program DOCK6.
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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.