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Full-Text Articles in Physical Sciences and Mathematics
Continuous Development Of Schemes For Parallel Computing Of The Electrostatics In Biological Systems: Implementation In Delphi, Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov
Continuous Development Of Schemes For Parallel Computing Of The Electrostatics In Biological Systems: Implementation In Delphi, Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov
Publications
Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) to include parallelization …
Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia
Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia
Publications
Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output …
Using Delphi Capabilities To Mimic Protein's Conformational Reorganization With Amino Acid Specific Dielectric Constants, Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov
Using Delphi Capabilities To Mimic Protein's Conformational Reorganization With Amino Acid Specific Dielectric Constants, Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov
Publications
Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to …