ArticleJournal of chemical information and modeling2013
Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach.
Article in Journal of chemical information and modeling, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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Who cites it
101 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
- Uncovering hidden druggable sites: computational approaches to allosteric and cryptic pocket discovery-from molecular dynamics to AI.Journal of computer-aided molecular design · 2026Review
- Probe-Atom Distributions Obtained from Mixed-Solvent Molecular Dynamics Improve the Scoring of Docking Calculations.Journal of chemical information and modeling · 2026Article
- Docking-score landscapes shape active-learning performance across Vina, Glide, and SILCS.Journal of computer-aided molecular design · 2026Article
- Drude SILCS-Nucleic: harnessing explicit electronic polarization in targeting RNA and DNA for drug design.Nucleic acids research · 2026Article
- Photoenzymatic Hydroalkylation Enables Streamlined Access to Aryl Glutarimide Precursors.Angewandte Chemie (International ed. in English) · 2026Article
- Article
- Computational Modeling of PROTAC Ternary Complexes as Ensembles Using SILCS-xTAC.Journal of chemical information and modeling · 2026Article
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.bioRxiv : the preprint server for biology · 2025Article
- Chasing allosteric inhibition of the SARS-CoV-2 PLpro via molecular dynamics simulations with flooding fragments (MDFFr).Journal of computer-aided molecular design · 2025Article
- GaSal-2: A Water-Soluble Antipseudomonal Agent Targeting the Extracellular Hemophore HasAp.ACS infectious diseases · 2025Article
- E-FTMap: A Protein Structure Based Pharmacophore Identification Server for Guiding Fragment Expansion.Journal of molecular biology · 2025Article
- CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis.Journal of chemical information and modeling · 2025Article
- CrypTothML: An Integrated Mixed-Solvent Molecular Dynamics Simulation and Machine Learning Approach for Cryptic Site Prediction.International journal of molecular sciences · 2025Article
- High-Throughput Ligand Dissociation Kinetics Predictions Using Site Identification by Ligand Competitive Saturation.Journal of chemical theory and computation · 2025Article
- Investigating the Interaction between Excipients and Monoclonal Antibodies PGT121 and N49P9.6-FR-LS: A Comprehensive Analysis.Molecular pharmaceutics · 2025Article
- Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation.Journal of chemical information and modeling · 2025Article
- Exploring Binding Sites in Chagas Disease Protein TcP21 Using Integrated Mixed Solvent Molecular Dynamics Approaches.Journal of chemical information and modeling · 2025Article
41 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
The site identification by ligand competitive saturation (SILCS) method identifies the location and approximate affinities of small molecular fragments on a target macromolecular surface by performing molecular dynamics (MD) simulations of the target in an aqueous solution of small molecules representative of different chemical functional groups. In this study, we introduce a set of small molecules to map potential interactions made by neutral hydrogen bond donors and acceptors and charged donor and acceptor fragments in addition to nonpolar fragments. The affinity pattern is obtained in the form of discretized probability or, equivalently, free energy maps, called FragMaps, which can be visualized with the target surface. We performed SILCS simulations for four proteins for which structural and thermodynamic data is available for multiple diverse ligands. Good overlap is shown between high affinity regions identified by the FragMaps and the crystallographic positions of ligand functional groups with similar chemical functionality, thus demonstrating the validity of the qualitative information obtained from the simulations. To test the ability of FragMaps in providing quantitative predictions, we calculate the previously introduced ligand grid free energy (LGFE) metric and observe its correspondence with experimentally measured binding affinity. LGFE is computed for different conformational ensembles and improvement in prediction is shown with increasing ligand conformational sampling. Ensemble generation includes a Monte Carlo sampling approach that uses the GFE FragMaps directly as the energy function. The results show that some but not all experimental trends are predicted and warrant improvements in the scoring methodology. In addition, the potential utility of atom-based free energy contributions to the LGFE scores and the use of multiple ligands in SILCS to identify displaceable water molecules during ligand design are discussed.
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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.