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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 …
The Role Of Protonation States In Ligand-Receptor Recognition And Binding, Marharyta Petukh, Shannon Stefl, Emil Alexov
The Role Of Protonation States In Ligand-Receptor Recognition And Binding, Marharyta Petukh, Shannon Stefl, Emil Alexov
Publications
In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and computational predictions that complex formation may involve titratable groups with unusual pKa’s and that protonation states frequently change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pHdependence of the binding. Indeed, experimental data strongly suggest that almost any binding is pH-dependent and to be correctly modeled, the protonation states must be properly assigned prior to and after the binding. One may accurately predict the protonation states when provided with the structures of the unbound …
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 …
In Silico Investigation Of Ph-Dependence Of Prolactin And Human Growth Hormone Binding To Human Prolactin Receptor, Lin Wang, Shawn Witham, Zhe Zhang, Michael E. Hodsdon, Emil Alexov
In Silico Investigation Of Ph-Dependence Of Prolactin And Human Growth Hormone Binding To Human Prolactin Receptor, Lin Wang, Shawn Witham, Zhe Zhang, Michael E. Hodsdon, Emil Alexov
Publications
Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that …