WELCOME TO PHEPS SERVER
The PHEPS Server is hosted by the Institute of Organic Chemistry, Biophysical Chemistry Lab at Bulgarian Academy of Sciences
The financial support comes from a collaborative project with Technical University - Sofia (TU-Sofia): grant D-002-126
Electrostatic computations of protein molecules implemented here are based on the electrostatic interaction methods and algorithms at our PHEPS server article published earlier in Nucleic Acids Research:
Kantardjiev,AA; Atanasov, BP, 2006, Nucleic Acids Research, 34:W43-W47.
A short introduction - fast pH-dependent electrostatic calculations
The server is supposed to be used mainly by protein scientists who need pH-dependent fast electrostatic analysis to explain their data. It is easy and straightforward to use.
The web server is based on fast self-consistent and iterative methods over many years in Biophysical Chemistry Lab. Its current version is written in C/C++ and Perl with Haskell extensions by one of us. Our package is capable of much more functionality and only basic electrostatic properties are presented online, the rest being under consideration for the next release.
The only input file is a coordinate file in PDB format either user supplied or just as a PDB ID, used to retrieve structure from our local PDB database. Following submission, the user is given some basic information about the protein molecule (chains; number of residues; ratio of ionogenic to all groups, Rel) and warned about certain inconsistencies in structure, related to subsequent calculation (interruption in residue numbering which might influence appearance of terminal charges). The user is given the possibility to edit initial setup of ionogenic groups (attention to CYS in SSBONDs and excluding covalently modified groups). This is accomplished by convenient interactive selection of ionogenic groups. Another option is to add missing terminal charges, fixed (non-titratable), whole or partial charges and titratable groups with user defined pKa intrinsic. All other parameters used as input are predefined or automatically calculated. After initial setup completion the calculation proceeds through several steps - evaluation of accessibilities and Born term, perturbation of pKa by partial charges and finally the iterative procedure for self-consistent evaluation of pK values. The obtained results are organized in two sections:
GLOBAL - net charge, electrostatic term of free energy, electrostatic potential distribution
LOCAL - proton population (degree of ionization of each i-th site), pK values, electrostatic energy of interaction of individual groups with whole multipole, electrostatic potential at user defined points
For each characteristic there is a link to web page. The contents of each page is comprised of the result itself, related derivatives (e.g. pI, pK½ etc) as well as a short description and examples for visualization of this type of data. All output data files are in standard plain text format. Visualization is straightforward with any 2-D plotting software and molecular graphics programs (RasMol, JMol, PyMol etc.).
Kantardjiev, AA; Atanasov, BP, 2009, Nucleic Acids Research, 37: W422-W427
You can access our new server with enhanced and new functionality at:
Protein Electric/Dipole Moment Tools
However PHEMTO is not just an upgrade of our server PHEPS. Inasmuch as biomolecules are a type of complex systems for which we nevertheless can calculate many properties from fundamental principles, Electric Dipole Moments occupy an unusual, if not unique, position in protein physics science. They may constitute an immensely valuable arena for investigating both the power and conceptual status of general principles of the way modern science relates atomic structure to function. To the best of our knowledge it is the first service for the community which allows pH-dependent electric dipole moment calculation - a crucial step in dissecting physical basis of protein interaction networks. In addition we implement in silico analysis of electrostatic mutants i.e. setting ionizable residues to neutral and exploring their effect on electrostatic interactions, pH dependence of molecular properties with special emphasis on electric dipole moments. Special attention is given to the ease of the service without sacrificing rigor of computational procedures.
Quantum Music of Biomolecules Project
You might want to have a glimpse at a new project:
Quantum Protein Project under development
Alexander Kantardjiev
Quantum Solitons mediated by Hydrogen Bonded Networks - Quantum Breathers
александър кантарджиев
alexkant@yahoo.com
.. Yet another CUDA quantum chemistry project - QUBIT - QUantum BIoinformatics Tools:
Computational task: CUDA quantum dynamics development for Hydrogen Bond Networks
Time-dependent Schrodinger equation solver for proton transfer GPU parallel implementation via CUFFT library Fast Fourier transform routines
... Graph theoretical analysis of Hydrogen Bond Network in Protein Molecules ( QUantum BIoinformatics Tools Server) :
Computational task: Application of graph theory algorithms for thorough analysis of Hydrogen Bond NetworksScientific task: Graph theory for charge transfer in Hydrogen Bond Networks
Coherence, entanglement, tunneling, solitons, tensor network states
Quantum Bioinformatics Tools (QUBIT) for HBN under development
