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We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational(More)
Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated(More)
We report here an efficient implementation of the finite difference Poisson-Boltzmann solvent model based on the Modified Incomplete Cholsky Conjugate Gradient algorithm, which gives rather impressive performance for both static and dynamic systems. This is achieved by implementing the algorithm with Eisenstat's two optimizations, utilizing the(More)
A major goal in neuroscience is the development of optical reporters of membrane potential that are easy to use, have limited phototoxicity, and achieve the speed and sensitivity necessary for detection of individual action potentials in single neurons. Here we present a novel, two-component optical approach that attains these goals. By combining DiO, a(More)
We have quantitatively studied the performance of a finite-difference Poisson-Boltzmann implicit solvent with respect to the TIP3P explicit solvent in a range of systems of biochemical interest. An overall agreement was found between the tested implicit and explicit solvents for hydrogen-bonding/salt-bridging dimers and peptide monomers and dimers of(More)
We have systematically analyzed a new nonpolar solvent model that separates nonpolar solvation free energy into repulsive and attractive components. Our analysis shows that either molecular surfaces or volumes can be used to correlate with repulsive free energies of tested molecules in explicit solvent with correlation coefficients higher than 0.99. In(More)
Continuum modeling of electrostatic interactions based upon the numerical solutions of the Poisson-Boltzmann equation has been widely adopted in biomolecular applications. To extend their applications to molecular dynamics and energy minimization, robust and efficient methodologies to compute solvation forces must be developed. In this study, we have first(More)
The optimizer developed for the Mining Minima algorithm, which uses ideas from Genetic Algorithms, the Global Underestimator Method, and Poling, has been adapted for use in ligand-receptor docking. The present study describes the resulting methodology and evaluates its accuracy and speed for 27 test systems. The performance of the new docking algorithm(More)
We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic carbons in all amino acids are united with carbons except those on Calpha. Our choice of explicit(More)