How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
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Summary
It can be concluded that a simple “generic” force field with a limited number of specific torsional parameters can describe intraand intermolecular interactions, although all comparison molecules were selected from the authors' 82-compound training set.
- Type
- article
- Published
- 2000-09-01
- Cited by
- 3,462
- References
- 64
- OpenAlex
- https://openalex.org/W2131288855
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:18831842
Keywords
Force field (fiction), Molecule, Test set, Ab initio, Basis set
References
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- General definition of ring puckering coordinates
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- Microwave spectra of deuterated ethanes: Internal rotation potential function and rz structure
- The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: How well is the x‐ray structure “maintained”?
- Advancing beyond the atom‐centered model in additive and nonadditive molecular mechanics
- UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
- Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
- Automated molecular mechanics parameterization with simultaneous utilization of experimental and quantum mechanical data
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- Visualisation of bioinformatics datasets
- QM/MM investigations of organic chemistry oriented questions.
- Simulation of the interaction between ScyTx and small conductance calcium-activated potassium channel by docking and MM-PBSA.
- Coupling between lysozyme and glycerol dynamics: microscopic insights from molecular-dynamics simulations.
- Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods.
- Solid-state NMR and MD simulations of the antiviral drug amantadine solubilized in DMPC bilayers.
- The implementation of a fast and accurate QM/MM potential method in Amber
- Molecular Dynamics as a pattern recognition tool: an automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site.
- Changes in non-core regions stabilise plastocyanin from the thermophilic cyanobacterium Phormidium laminosum
- The Therapeutically Anti-prion Active Antibody-fragment scFv-W226: Paramagnetic Relaxation-Enhanced NMR Spectroscopy aided Structure Elucidation of the Paratope-epitope Interface
- Insights into nucleotide recognition by cell division protein FtsZ from a mant-GTP competition assay and molecular dynamics.
- The maize ALDH protein superfamily: linking structural features to functional specificities
- Differential molecular information of maurotoxin peptide recognizing IKCa and Kv1.2 channels explored by computational simulation
- N-Glycoform Diversity of Cellobiohydrolase I from Penicillium decumbens and Synergism of Nonhydrolytic Glycoform in Cellulose Degradation*
- Enhancing the melting properties of small molecule-DNA hybrids through designed hydrophobic interactions: an experimental-computational study.
- Genome‐wide Inference of Transcription Factor–DNA Binding Specificity in Cell Regeneration Using a Combination Strategy
- Insights into the potential aggregation liabilities of the b12 Fab fragment via elevated temperature molecular dynamics.
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