ArticleJournal of chemical information and modeling2023
SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers, 2 of them syntheses that pooled it.
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Who cites it
107 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Anti-inflammatory mechanism of resveratrol's Triglyceride-lowering effect in hyperlipidemia: a meta-analysis integrated network pharmacology and molecular dynamics simulation.Clinical and experimental medicine · 2025Pooled it
- Synthesis, characterization, crystal structures, antitumor activity, and computational study of novel thiosemicarbazone derivatives from thiazol-2/5-carbaldehyde.RSC advances · 2026Article
- Thiolactomycin-based morpholino and piperidino conjugates: synthesis, antimalarial evaluation, and PResearch in pharmaceutical sciences · 2026Article
- Large-scale comparative virtual screening identifies novel molecular targets underlying the multi-target activity of quercetin in psoriasis.Inflammopharmacology · 2026Article
- Anti-Inflammatory Activity of Cotula cinerea Essential Oil: Integrated Chemical, In Vivo, Histological, and Computational Evaluation.Chemistry & biodiversity · 2026Article
- Expanding the chemical space of Bcl-2 inhibitors: a multiscale computational exploration of the benzopyran (chromene) scaffold.Journal of molecular modeling · 2026Article
- Quantum-mechanical insights into sodium alginate gelation and AI-driven discovery of synthetic biomimetic analogs.Journal of computer-aided molecular design · 2026Article
- Exploring the Inhibitory Effects of Some Detergents onACS omega · 2026Article
- β-Thujaplicin modulates the ODC-ROS-linked apoptosis in H460 lung cancer cells.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Integration of network pharmacology, structure-based pharmacophore modeling, DFT, molecular docking, and molecular dynamics simulations to identify multi-target small molecule inhibitors against Alzheimer's disease.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field.Journal of chemical information and modeling · 2026Article
- Computational discovery and dynamic profiling of dual acetylcholinesterase and monoacylglycerol lipase inhibitors for Alzheimer's disease.Molecular diversity · 2026Article
- Crocetin Halts Tumorigenesis in Metastatic Breast Cancer via Disrupting CYP2J2/EET Axis.ACS omega · 2026Article
- Article
- Ocotea odorifera extract: antimicrobial and antibiofilm activities, phytochemical aspects, cytotoxicity and anti-inflammatory potential of an endangered plant species.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- Protective Effects of the Ethanolic Leaf Extract ofMolecules (Basel, Switzerland) · 2026Article
- Artificial Intelligence- and Machine Learning-Assisted Structure-Based Virtual Screening of Compounds That Target 15PGDH.Pharmaceutics · 2026Article
- Integrative crystallography and molecular dynamics reveal isoform-specific ligand interaction networks in C4 and nonC4 plant NADP-malic enzyme.The Plant journal : for cell and molecular biology · 2026Article
- Multiclass Machine Learning-Based Discovery of Novel Scaffold Inhibitors Targeting ALK.Pharmaceuticals (Basel, Switzerland) · 2026Article
47 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most steps of drug discovery are now routinely supported and accelerated by computer-aided drug design tools. Among them, structure-based approaches use the three-dimensional structure of the targeted biomacromolecule as a major source of information. When it comes to calculating the interactions of small molecules with proteins using the equations of molecular mechanics, topologies, atom typing, and force field parameters are required. However, generating parameters for small molecules remains challenging due to the large number of existing chemical groups. The SwissParam web tool was first released in 2011 with the aim of generating parameters and topologies for small molecules based on the Merck molecular force field (MMFF) while being compatible with the CHARMM22/27 force field. Here, we present an updated version of SwissParam, providing various new features, including the possibility to setup covalent ligands. Molecules can now be imported from different file formats or via a molecular sketcher. The MMFF-based approach has been updated to provide parameters and topologies compatible with the CHARMM36 force field. An option was added to generate small molecule parametrizations following the CHARMM General Force Field via the multipurpose atom-typer for CHARMM (MATCH) approach. Additionally, SwissParam now generates information on probable alternative tautomers and protonation states of the query molecule so that the user can consider all microspecies relevant to its compound. The new version of SwissParam is freely available at www.swissparam.ch and can also be accessed through a newly implemented command-line interface.
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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.