Karin Wichmann

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We present a combination of semiempirical quantum-mechanical (SQM) calculations in the conductor-like screening model with the MM/GBSA (molecular-mechanics with generalized Born and surface-area solvation) method for ligand-binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen-bond corrections and two(More)
The COSMO surface polarization charge density σ resulting from quantum chemical calculations combined with a virtual conductor embedding has been widely proven to be a very suitable descriptor for the quantification of interactions of molecules in liquids. In a preceding paper, grid-based local histograms of σ have been introduced in the COSMOsim3D method,(More)
[5] Tatsuya Akutsu. A polynomial time algorithm for finding a largest common sub-graph of almost trees of bounded degree. [6] Tatsuya Akutsu. Protein structure alignment using dynamic programming and iterative improvement. Fujiyama. Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm.(More)
The Conductor-Like-Screening-Model for Real Solvents (COSMO-RS) method has been used for the blind prediction of cyclohexane-water distribution coefficients logD within the SAMPL challenge. The partition coefficient logP of the neutral species was calculated first and then corrected for dissociation or protonation, as appropriate for acidic or basic(More)
Theory, validation, and applications of a novel approach for the quantification of drug similarity – COSMOsim-are described. This structure-free method uses the surface polarities as defined in the quantum chemically based conductor-like screening model for realistic solvation (COSMO-RS). The histograms of these surface polarities, the so-called sigma(More)
By the practical success of the COSMO-RS fluid phase thermodynamics model [1,2] in many areas of chemistry , the COSMO polarization charge densities s have been proven to be excellent descriptors for the quantifi-cation of the most important kinds of molecular interactions in the liquid phase, as polar interactions, hydrogen bonding and hydrophobicity. In(More)
COSMO σ-surfaces resulting from quantum chemical calculations of molecules in a simulated conductor, and their histograms, the so-called σ-profiles, are widely proven to provide a very suitable and almost complete basis for the description of molecular interactions in condensed systems. The COSMOsim method therefore introduced a global measure of molecular(More)
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