A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197

By W. Cornell, P. Cieplak, C. Bayly, I. Gould, Kenneth M. Merz Jr., D. Ferguson, D. Spellmeyer, T. Fox, Anddanielr . Caldwell, Peter A. Kollman. 1996

Subfields: Optimization & Training

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Optimization & Training

Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, methodology): “Among the diverse available force-fields, AMBER [104], CHARMM [105] and GROMOS [106], can be highlighted as widely used in molecular dynamics simulations.”
An overview of the Amber biomolecular simulation package (2013, background): “(3) Quantum instanton54–56 is a theoretical approach for computing thermal reaction rates in complex molecular systems, based on the semiclassical instanton approximation (QI).”
Characterizing elastic properties of carbon nanotubes/polyimide nanocomposites using multi-scale simulation (2010, unknown): “The constants kr 1⁄4 93;800 kcal mol nm2 and kh 1⁄4 126 kcal mol rad(2) selected from AMBER force field for carbon–carbon atomic interaction [15], were employed in the present molecular simulation.”
Comparison of multiple Amber force fields and development of improved protein backbone parameters (2006, methodology): “The ‘‘Cornell et al.’’ force field 5 (denoted as ff94 in Amber) has been the most widely used with the Amber suite of programs 6,7 since its publication over a decade ago.”
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. (2003, methodology): “force-field.(115) Bonded parameters for the triphosphate moiety of GTP were taken from Leach & Klein(116) and atomic partial charges for GTP(42) were derived using the RESP procedure.”
Machine learning exciton dynamics (2015, unknown): “The MD runs were carried out using the NAMD software package [46] with the AMBER99 force field (ff99SB) [47].”
Structure guided forcefield optimization (2011, unknown): “(5)] can be directly subtracted from the potential term at each iteration:”
TTD: Therapeutic Target Database (2002, background): “Development of advanced computational methods for bioinformatics (4), molecular modeling (8), drug design and pharmacokinetics analysis (9–11) increasingly uses known therapeutic targets to refine and test algorithms and parameters.”