Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs
نویسندگان
چکیده
منابع مشابه
Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins
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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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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ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2018
ISSN: 1549-9618,1549-9626
DOI: 10.1021/acs.jctc.8b00413