Allows the display of molecular surfaces of moving (or still) proteins, putting special emphasis on their electrical and lipophilic properties. BioBlender is an extension of Blender. The software provides various types of visualization for the analysis of proteins structures: alpha carbon, main chain, main chain and side chains, all atoms (including hydrogens) and molecular surface. It can help to understand the dynamical forces governing intermolecular interactions and thus facilitate new insights and discoveries.
Uses as a Virtual logP calculator. The Virtual logP is obtained by the Molecular Lipophilicity Potential (MLP) that is calculated projecting the Broto-Moreau lipophilicity atomic constants on the molecular surface. Because the MLP is sensitive to conformational effects, the logP prediction requires a 3D structure with full hydrogens as input. For better results, the logP should be calculated for all most interesting conformations obtained by an exhaustive conformational analysis.
Offers the possibility to predict the phospholipophilicity of all compounds included in PubChem collection as log kw of both MG and DD2 chromatographic columns. Log kwIAM.MG/DD2 is a free on-line service aimed at calculating log kW immobilized artificial membrane (IAM) values of any molecule. A wide set of physico-chemical and topological properties have been taken into account yielding a robust final model including: (i) a parameter referring to lipophilicity, (ii) a parameter accounting for hydrophilic/lipophilic balance of the analyte, (iii) a parameter accounting for molecular size, and (iv) a parameter accounting for molecule flexibility.
Assists in collecting, classifying, and analyzing metabolic reactions. VEGA ZZ is a program representing a versatile engine to develop in-house targeted applications for metabolism analysis and prediction. It provides a method for displaying 3D structure of a substrate allowing the selection of the atoms involved in a given reaction.
Provides various kinds of Molecular Lipophilicity Potential (MLP)-based tools to use within the popular 3D visualization software PyMOL. The MLP Tools plugin is a comprehensive collection of useful programs in a high graphic quality environment that apply the MLP to quickly visualize color-coded lipophilicity around molecules or in binding pockets and to quantify this lipophilicity. MLP Tools can also be used to map lipophilic properties on solvent accessible surfaces of both small molecules and proteins.
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