ArticleJournal of chemical theory and computation2010
Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed.
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- Poly(ADP-ribose) (PAR) exhibits ion-dependent structural properties distinct from RNA.Nucleic acids research · 2026Article
- Solvation Energetic Costs of Cognate Binding Site Formation.Journal of chemical information and modeling · 2025Article
- Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set.Journal of chemical information and modeling · 2025Article
- Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.Journal of chemical information and modeling · 2025Article
- Experimental and computational investigations of RNA duplexes containing N7-regioisomers of adenosine and LNA-adenosine.Nucleic acids research · 2025Article
- Molecular Docking of Endolysins for Studying Peptidoglycan Binding Mechanism.Molecules (Basel, Switzerland) · 2024Article
- Sugar mimics and their probable binding sites: design and synthesis of thiazole linked coumarin-piperazine hybrids as galectin-1 inhibitors.RSC advances · 2024Article
- Structure and dimerization properties of the plant-specific copper chaperone CCH.Scientific reports · 2024Article
- Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases.Journal of chemical information and modeling · 2024Article
- Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites.Journal of chemical theory and computation · 2024Article
- AmberTools.Journal of chemical information and modeling · 2023Article
- Mechanism of Asparagine-Mediated Proton Transfer in Photosynthetic Reaction Centers.Biochemistry · 2023Article
- Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction.Molecules (Basel, Switzerland) · 2023Article
- Dynamic docking of small molecules targeting RNA CUG repeats causing myotonic dystrophy type 1.Biophysical journal · 2023Article
- Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls.Journal of chemical information and modeling · 2022Article
- RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.The journal of physical chemistry. B · 2022Article
- Molecular Modeling in Anion Exchange Membrane Research: A Brief Review of Recent Applications.Molecules (Basel, Switzerland) · 2022Review
- Implementation and Optimization of the Embedded Cluster Reference Interaction Site Model with Atomic Charges.The journal of physical chemistry. A · 2022Article
- Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.Physical chemistry chemical physics : PCCP · 2022Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G.
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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.