ArticleJournal of computer-aided molecular design2014
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling.
Article in Journal of computer-aided molecular design, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Computer-Aided Drug Design for Type 2 Diabetes-Related Enzymes: SILCS-Based Fragment Mapping, Pharmacophore Modeling, and Virtual Screening.Journal of chemical information and modeling · 2026Article
- Automated pharmacophore hypothesis generator for SILCS-Pharm: ph4gen.Journal of computer-aided molecular design · 2026Article
- In silico designing of small molecules for targeting RNA: current landscape and future directions.Journal of computer-aided molecular design · 2026Review
- Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation.Journal of chemical information and modeling · 2025Article
- Modeling Ligand Binding Site Water Networks with Site Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities.Journal of chemical theory and computation · 2024Article
- Enhancing SILCS-MC via GPU Acceleration and Ligand Conformational Optimization with Genetic and Parallel Tempering Algorithms.The journal of physical chemistry. B · 2024Article
- Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART).Journal of cheminformatics · 2024Article
- Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation.Journal of chemical theory and computation · 2023Article
- Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein Charge Prediction.Molecular pharmaceutics · 2023Article
- Computer-Aided Drug Design: An Update.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Nitro-benzylideneoxymorphone, a bifunctional mu and delta opioid receptor ligand with high mu opioid receptor efficacy.Frontiers in pharmacology · 2023Article
- hERG Blockade Prediction by Combining Site Identification by Ligand Competitive Saturation and Physicochemical Properties.Chemistry (Basel, Switzerland) · 2022Article
- Mapping the binding sites of challenging drug targets.Current opinion in structural biology · 2022Review
- FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures.Journal of molecular biology · 2022Article
- ELIXIR-A: An Interactive Visualization Tool for Multi-Target Pharmacophore Refinement.ACS omega · 2022Article
- Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.New journal of chemistry = Nouveau journal de chimie · 2022Article
- Rapid and accurate estimation of protein-ligand relative binding affinities using site-identification by ligand competitive saturation.Chemical science · 2021Article
- Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics.Journal of chemical information and modeling · 2021Article
- Article
- Discovery of beta-lactamase CMY-10 inhibitors for combination therapy against multi-drug resistant Enterobacteriaceae.PloS one · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Database screening using receptor-based pharmacophores is a computer-aided drug design technique that uses the structure of the target molecule (i.e. protein) to identify novel ligands that may bind to the target. Typically receptor-based pharmacophore modeling methods only consider a single or limited number of receptor conformations and map out the favorable binding patterns in vacuum or with a limited representation of the aqueous solvent environment, such that they may suffer from neglect of protein flexibility and desolvation effects. Site-Identification by Ligand Competitive Saturation (SILCS) is an approach that takes into account these, as well as other, properties to determine 3-dimensional maps of the functional group-binding patterns on a target receptor (i.e. FragMaps). In this study, a method to use the FragMaps to automatically generate receptor-based pharmacophore models is presented. It converts the FragMaps into SILCS pharmacophore features including aromatic, aliphatic, hydrogen-bond donor and acceptor chemical functionalities. The method generates multiple pharmacophore hypotheses that are then quantitatively ranked using SILCS grid free energies. The pharmacophore model generation protocol is validated using three different protein targets, including using the resulting models in virtual screening. Improved performance and efficiency of the SILCS derived pharmacophore models as compared to published docking studies, as well as a recently developed receptor-based pharmacophore modeling method is shown, indicating the potential utility of the approach in rational drug design.
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