Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions.

By Wei Wang, Oreola Donini, Carolina Reyes, Peter A. Kollman. Annual Review of Biophysics and Biomolecular Structure, 2001

521 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cec34b560386caf3de1fb28f96175e68e399882f

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In Materials Chemistry

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Citations in the corpus

Mechanics of biomolecules (2002, background): “…(MD) simulations are based upon numerical solutions of the classical Newtonian equations of motion in which the force exerted on each atom is given by the negative gradient of the potential energy function with respect to the position of the atom (McCammon and Harvey, 1987; Wang et al., 2001).”
The Poisson–Boltzmann equation for biomolecular electrostatics: a tool for structural biology (2002, background): “…by Kollman and coworkers for post-processing molecular dynamics trajectories without having to consider solvent coordinates (Kollman et al., 2000; Wang et al., 2001 and references cited therein) providing strong evidence for the accuracy of the methodology (Lee et al., 2001) pH dependent…”
Molecular and Cellular Biophysics: Index (2006, background): “More work with such hybrid models shows great promise in dissecting the contributions of various enzyme– substrate interactions in the reduction of Ey (Wang et al., 2001).”
Advances and Challenges in Protein-Ligand Docking (2010, methodology): “and OWFEG are computationally expensive [88].”
Theoretical and computational hierarchical nanomechanics of protein materials: Deformation and fracture (2008, methodology): “The CHARMM force field belongs to a class of models with similar descriptions of the interatomic forces; other models include the DREIDING force field [58], the UFF force field [59], or the AMBER model [52,53,60].”
Identification of functionally conserved residues with the use of entropy–variability plots (2003, methodology): “9–14 Other groups have predicted functional motifs from an analysis of protein interaction surfaces using principal component analysis, 15 analysis of physicochemical descriptors to score protein– protein interactions, 16 search for motifs in Blocks databases, 17 or alignment of hinge regions.”