ReviewMolecules (Basel, Switzerland)2018
Solvents to Fragments to Drugs: MD Applications in Drug Design.
Review in Molecules (Basel, Switzerland), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- New strategies to enhance the efficiency and precision of drug discovery.Frontiers in pharmacology · 2025Review
- Exploring an Intracellular Allosteric Site of CC-Chemokine Receptor 4 from 3D Models, Probe Simulations, and Mutagenesis.ACS pharmacology & translational science · 2024Article
- Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN.Nature communications · 2024Article
- PLAS-20k: Extended Dataset of Protein-Ligand Affinities from MD Simulations for Machine Learning Applications.Scientific data · 2024Article
- Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97.Communications chemistry · 2022Article
- Mechanistic Insight into the Binding of Huperzine a with Human Transferrin: Computational, Spectroscopic and Calorimetric Approaches.ACS omega · 2022Article
- Imidazole and nitroimidazole derivatives as NADH-fumarate reductase inhibitors: Density functional theory studies, homology modeling, and molecular docking.Journal of computational chemistry · 2022Article
- Evaluating the use of absolute binding free energy in the fragment optimisation process.Communications chemistry · 2022Article
- Cosolvent Sites-Based Discovery ofJournal of medicinal chemistry · 2022Article
- Computational Design of Inhibitors Targeting the Catalytic β Subunit ofAntibiotics (Basel, Switzerland) · 2022Article
- Extracting Atomic Contributions to Binding Free Energy Using Molecular Dynamics Simulations with Mixed Solvents (MDmix).Current drug discovery technologies · 2022Article
- Ten things I `hate' about refinement.Acta crystallographica. Section D, Structural biology · 2021Article
- Structure-based molecular modeling in SAR analysis and lead optimization.Computational and structural biotechnology journal · 2021Review
- Biased Docking for Protein-Ligand Pose Prediction.Methods in molecular biology (Clifton, N.J.) · 2021Article
- The rise of molecular simulations in fragment-based drug design (FBDD): an overview.Drug discovery today · 2020Review
- Computational approaches for drug discovery against trypanosomatid-caused diseases.Parasitology · 2020Review
- Allosteric Binding Sites On Nuclear Receptors: Focus On Drug Efficacy and Selectivity.International journal of molecular sciences · 2020Article
- Molecular Modeling in Drug Design.Molecules (Basel, Switzerland) · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Simulations of molecular dynamics (MD) are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: Binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals solvent structures and preferential interaction sites (hot spots) on the protein surface. The information provided by water and its cosolvents can be used very effectively to understand protein ligand recognition and to improve the predictive capability of well-established methods such as molecular docking. The application of MD simulations to the study of the association of proteins with drug-like compounds is currently only possible for specific cases, as it remains computationally very expensive and labor intensive. MDmix simulations on the other hand, can be used systematically to address some of the common tasks in SBDD. With the advent of new tools and faster computers we expect to see an increase in the application of mixed solvent MD simulations to a plethora of protein targets to identify new drug candidates.
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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.