How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

By Junmei Wang, P. Cieplak, Peter A. Kollman. Journal of Computational Chemistry, 2000

3,452 citations recorded by the source corpus.

Subfields: Molecular Biology, Physical and Theoretical Chemistry, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/ba53f5999d773690c7a0dacab3a7c051737b5448

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In Molecular Biology

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5. Alexander Schug
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In Physical and Theoretical Chemistry

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In Spectroscopy

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6. Martin Weigt
7. H. Szurmant
8. Alexander Schug

Citations in the corpus

• Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. (2005, methodology): “2 were applied to 1–4 Lennard-Jones and Coulombic interactions, respectively, as described for AMBER all-atom potentials (Cornell et al., 1995; Duan et al., 2003; Kollman et al., 1997; Wang et al., 2000).”
• Computational modeling of phosphotransfer complexes in two-component signaling. (2010, methodology): “Here, we use AmberF99 (Wang et al ., 2000) (http://chemistry.csulb.edu/ffamber) with explicit Tip3p solvent and coun-terions ( Jorgensen et al ., 1983), a time step of 0.002 fs, and particle mesh Eswalds electrostatics (Essmann et al ., 1995).”
• PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations (2007, positive): “PDB2PQR currently allows users to assign protein and (where available) nucleic acid parameters based on explicit solvent AMBER99 (19) and CHARMM27 (20) force fields, the PARSE continuum electrostatics force field (21), a Poisson–Boltzmann-optimized force field by Tan et al.”
• High-resolution protein complexes from integrating genomic information with molecular simulation (2009, methodology): “AmberF99simulationsforrelaxation.”
• PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations (2004, neutral): “Currently, PDB2PQR provides parameters from CHARMM22 (19), AMBER99 ( 20 ) or PARSE (21) force fields.”
• Force fields for protein simulations. (2003, background): “Some account of the longer-range effects was provided in subsequent parameterizations, referred to as ff96 (Kollman et al., 1997) and ff99 (Wang et al., 2000), in which the and potentials were fit to tetrapeptide as well as dipeptide quantum mechanical conformational energies.”