منابع مشابه
Two-Stage SVR Approach for Predicting Accessible Surface Areas of Amino Acids
We address the problem of predicting solvent accessible surface area (ASA) of amino acid residues in protein sequences, without classifying them into buried and exposed types. A two-stage support vector regression (SVR) approach is proposed to predict real values of ASA from the position-specific scoring matrices (PSSMs) generated from PSI-BLAST profiles. By adding SVR as the second stage to ca...
متن کاملAtomic environment energies in proteins defined from statistics of accessible and contact surface areas.
Atomic contact potentials are derived by statistical analysis of atomic surface contact areas versus atom type in a database of non-homologous protein structures. The atomic environment is characterized by the surface area accessible to solvent and the surface of contacts with polar and non-polar atoms. Four types of atoms are considered, namely neutral polar atoms from protein backbones and fr...
متن کاملTwo-stage support vector regression approach for predicting accessible surface areas of amino acids.
We address the problem of predicting solvent accessible surface area (ASA) of amino acid residues in protein sequences, without classifying them into buried and exposed types. A two-stage support vector regression (SVR) approach is proposed to predict real values of ASA from the position-specific scoring matrices generated from PSI-BLAST profiles. By adding SVR as the second stage to capture th...
متن کاملExact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules
A new method for exact analytical calculation of the accessible surface areas and their gradients with respect to atomic coordinates is described. The new surface routine, GETAREA, finds solvent-exposed vertices of intersecting atoms, and thereby avoids calculating buried vertices which are not needed to determine the accessible surface area by the Gauss]Bonnet theorem. The surface routine was ...
متن کاملAn extended aqueous solvation model based on atom-weighted solvent accessible surface areas: SAWSA v2.0 model.
A new method is proposed for calculating aqueous solvation free energy based on atom-weighted solvent accessible surface areas. The method, SAWSA v2.0, gives the aqueous solvation free energy by summing the contributions of component atoms and a correction factor. We applied two different sets of atom typing rules and fitting processes for small organic molecules and proteins, respectively. For...
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ژورنال
عنوان ژورنال: Nature
سال: 1952
ISSN: 0028-0836,1476-4687
DOI: 10.1038/169269a0