99,183 research outputs found
The Journal of Computer-Aided Molecular Design: a bibliometric note
Summarizes the articles in, and the citations to, volumes 2-24 of the Journal of Computer-Aided Molecular Design. The citations to the journal come from almost 2000 different sources that span a very wide range of academic subjects, with the most heavily cited articles being descriptions of software systems and of computational methods
Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations
Atomic radii and charges are two major parameters used in implicit solvent
electrostatics and energy calculations. The optimization problem for charges
and radii is under-determined, leading to uncertainty in the values of these
parameters and in the results of solvation energy calculations using these
parameters. This paper presents a new method for quantifying this uncertainty
in implicit solvation calculations of small molecules using surrogate models
based on generalized polynomial chaos (gPC) expansions. There are relatively
few atom types used to specify radii parameters in implicit solvation
calculations; therefore, surrogate models for these low-dimensional spaces
could be constructed using least-squares fitting. However, there are many more
types of atomic charges; therefore, construction of surrogate models for the
charge parameter space requires compressed sensing combined with an iterative
rotation method to enhance problem sparsity. We demonstrate the application of
the method by presenting results for the uncertainties in small molecule
solvation energies based on these approaches. The method presented in this
paper is a promising approach for efficiently quantifying uncertainty in a wide
range of force field parameterization problems, including those beyond
continuum solvation calculations.The intent of this study is to provide a way
for developers of implicit solvent model parameter sets to understand the
sensitivity of their target properties (solvation energy) on underlying choices
for solute radius and charge parameters
Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections
Molecular Density Functional Theory (MDFT) offers an efficient implicit-
solvent method to estimate molecule solvation free-energies whereas conserving
a fully molecular representation of the solvent. Even within a second order ap-
proximation for the free-energy functional, the so-called homogeneous reference
uid approximation, we show that the hydration free-energies computed for a
dataset of 500 organic compounds are of similar quality as those obtained from
molecular dynamics free-energy perturbation simulations, with a computer cost
reduced by two to three orders of magnitude. This requires to introduce the
proper partial volume correction to transform the results from the grand
canoni- cal to the isobaric-isotherm ensemble that is pertinent to experiments.
We show that this correction can be extended to 3D-RISM calculations, giving a
sound theoretical justifcation to empirical partial molar volume corrections
that have been proposed recently.Comment: Version with correct equation numbers is here:
http://compchemmpi.wikispaces.com/file/view/sergiievskyi_et_al.pdf/513575848/sergiievskyi_et_al.pdf
Supporting information available online at:
http://compchemmpi.wikispaces.com/file/view/SuppInf_sergiievskyi_et_al_07-04-2014.pdf/513576008/SuppInf_sergiievskyi_et_al_07-04-2014.pd
- …