Analytical approximation to the accessible surface area of proteins
نویسندگان
چکیده
منابع مشابه
Joint neighbors approximation of macromolecular solvent accessible surface area
A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and the...
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We present faster sequential and parallel algorithms for computing the solvent accessible surface area (ASA) of protein molecules. The ASA is computed by finding the exposed surface areas of the spheres obtained by increasing the van der Waals’ radii of the atoms with the van der Waals’ radius of the solvent. Using domain specific knowledge, we show that the number of sphere intersections is on...
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In the calculation of thermodynamic properties and three-dimensional structures of macromolecules, such as proteins, it is important to have an efficient algorithm for computing the solvent-accessible surface area of macromolecules. Here, we propose a new analytical method for this purpose. In the proposed algorithm we consider the transformation that maps the spherical circles formed by inters...
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SUMMARY RVP-net is an online program for the prediction of real valued solvent accessibility. All previous methods of accessible surface area (ASA) predictions classify amino acid residues into exposure states and named them buried or exposed based on different thresholds. Real values in some cases were generated by taking the mid points of these state thresholds. This is the first method, whic...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 1980
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.77.4.1736