منابع مشابه
QM quality atomic charges for proteins
The concept of atomic point charges is well established in theoretical chemistry. Atomic point charges have played an important role in understanding and modeling chemical behavior by allowing to extract and quantify information stored in the molecular electron distribution of chemical compounds. Thus, atomic point charges have been used to estimate reactivity indices, dissociation constants, p...
متن کاملHigh-quality and universal empirical atomic charges for chemoinformatics applications
BACKGROUND Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinformatics, as they are informative descriptors that can be utilised in pharmacophore design, virtual screening, similarity searches etc. Especially conformationally-dependent charge...
متن کاملPartial atomic charges of amino acids in proteins.
Using a semiempirical quantum mechanical procedure (FCPAC) we have calculated the partial atomic charges of amino acids from 494 high-resolution protein structures. To analyze the influence of the protein's environment, we considered each residue under two conditions: either as the center of a tripeptide with PDB structure geometry (free) or as the center of 13-16 amino acid clusters extracted ...
متن کاملA comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities.
Recently we reported a combined QM/MM approach to estimate condensed-phase values of atomic polarizabilities for use in (bio)molecular simulation. The setup relies on a MM treatment of the solvent when determining atomic polarizabilities to describe the response of a QM described solute to its external electric field. In this work, we study the effect of using alternative descriptions of the so...
متن کاملOrganizing atomic partial charges into a database
A partial charge database was constructed for 117 molecules. The actual database contains Mulliken, natural population analysis, and stockholder atomic charges calculated from the HF/6-31G(d) or HF/6-311þG(2d,p) wavefuntions. The MP2/631G(d), B3LYP/6-31G(d), or HF/6-31G(d) equilibrium geometries were used for these calculations. The database also contains the corresponding total energies calcul...
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ژورنال
عنوان ژورنال: Journal of Cheminformatics
سال: 2014
ISSN: 1758-2946
DOI: 10.1186/1758-2946-6-s1-p61