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Automates the process of calculating pKa, protonation states and titration curves of ionizable groups in macromolecules, given an atomic resolution structure as input. The output structure contains missing hydrogens added according to calculated protonation states and is available in several formats used by a number of popular molecular modeling packages. The calculations are based on the standard continuum solvent methodology , within the frameworks of either the generalized Born (GB) or the Poisson–Boltzmann (PB) models (user-specified). All steps of the computational process are fully automated. Commonly used input parameters are accessible via a simple interface that provides reasonable defaults.
PBEQ Solver / Poisson-Boltzmann-Equations Solver
Provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential. PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein–protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue. It also uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference PB equation of molecules specified by users.
Allows analysis of pH-dependent electric/dipole moments. Subtle.Nets is a web server that allows users to compare their results against theoretical data as well to get deeper insights and enlightment in the way protein structure relays function. It includes several features such as separation of contribution from permanent and ionic (pH-dependent) charges, or elicitation of interplay of dipole/electric moments in protein–protein recognition and structure formation. The software is suitable for first acquaintance and training in the field of theoretical biophysics.
Provides a useful method for basic academic study and industrial application of acidic and alkaline enzymes. AcalPred is a free online server that discriminates acidic enzymes. An ANOVA-based feature selection technique was utilized to optimize dipeptide compositions for improving the prediction capability of this model. An overall accuracy of 96 per cent was achieved, demonstrating that AcalPred can be used as a powerful tool for the study of enzymes in the adaptation to acidic or alkaline environment.
Draws a protein charge plot. charge reads a protein sequence and writes a file (or plots a graph) of the mean charge of the amino acids within a window of specified length as the window is moved along the sequence. The algorithm uses the column "charge" from a datafile (Eamino.dat) of amino acid properties. It gives the residues 'D' and 'E' a charge of -1, 'K' and 'R' a charge of +1, and the residue 'H' a charge of +0.5. Then it calculates the mean charge across the window, which by default is 5 residues.
Predicts sets of point mutations that will change the pKa values of a set of target residues in a given direction, thus allowing for targeted re-design of the pH-dependent characteristics of proteins. The server provides the user with an interactive experience for re-designing pKa values by pre-calculating pKa values from all feasible point mutations. Design solutions are found in less than 10 min for a typical design job for a medium-sized protein. Mutant pKa values calculated by the pKD web server are in close agreement with those produced by comparing results from full-fledged pKa calculation methods.
PHEPS / pH-dependent Protein Electrostatics Server
A web service for fast prediction and experiment planning support, as well as for correlation and analysis of experimentally obtained results, reflecting charge-dependent phenomena in globular proteins. Its implementation is based on long-term experience (PHEI package) and the need to explain measured physicochemical characteristics at the level of protein atomic structure. The approach is semi-empirical and based on a mean field scheme for description and evaluation of global and local pH-dependent electrostatic properties: protein proton binding; ionic sites proton population; free energy electrostatic term; ionic groups proton affinities (pKa,i) and their Coulomb interaction with whole charge multipole; electrostatic potential of whole molecule at fixed pH and pH-dependent local electrostatic potentials at user-defined set of points.
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