Surface Generalized Born Method: A Simple, Fast, and Precise Implicit

We present the surface generalized born (S-GB) method, based on expansion of energy in a surface integral series. The method can be parametrized for ...

Jul 7, 2015 - In an effort to create a more accurate model for nucleic acids, a similar procedure to the development of GB-neck2 is described here for nucleic acids. The resulting ... My-Tra Le , Wojciech K Kasprzak , Taejin Kim , Feng Gao , Megan YL

Sep 28, 2011 - challenge efficient parallel performance of generalized Born implicit solvent algorithms. Here, we report how NAMD, a parallel molecular ...

Sep 28, 2011 - Accurate electrostatic descriptions of aqueous solvent are critical for simulation studies of biomolecules, but the computational cost of explicit ...

Jul 7, 2015 - Production runs were performed in the NVT ensemble. Data Analysis. Backbone RMSD (BB-RMSD) and cluster analysis (k-means algorithm) were carried out by the ptraj and cpptraj(61) programs in Ambertools version 12 and 14.(23b, 23c) The tr

Jul 7, 2015 - Sherry Bermeo,. § and Carlos Simmerling*,†,‡. †. Department of Chemistry,. ‡. Laufer Center for Physical and Quantitative Biology, and. §.

Jul 7, 2015 - The Generalized Born (GB) implicit solvent model has undergone significant improvements in accuracy for modeling of proteins and small ...

Lei Xu , Huiyong Sun , Youyong Li , Junmei Wang , and Tingjun Hou. The Journal of Physical Chemistry B 2013 117 (28), 8408-8421. Abstract | Full Text HTML ...

The SMARTS language is used for the exact definition of atoms types, and Ullmann's ... Journal of Chemical Information and Modeling 2018 58 (2), 271-286.

Differential Geometry-Based Solvation and Electrolyte Transport Models for Biomolecular Modeling: A Review. Guo Wei , Nathan Baker. 2016,417-461 ...