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Protein pKa prediction software tools | Sequence analysis

The pH-dependence of enzymatic activity and protein stability is of major importance for the biological function and industrial application of enzymes and proteins.Source text:(Tynan-Connolly et al., 2006) pKD: re-designing protein pKa values.…
DelPhiPKa
Desktop
Web

DelPhiPKa

A pKa prediction web server which implements DelPhi Gaussian dielectric…

A pKa prediction web server which implements DelPhi Gaussian dielectric function to calculate electrostatic potentials generated by charges of biomolecules. Topology parameters are extended to…

PBEQ Solver
Web

PBEQ Solver Poisson-Boltzmann-Equations Solver

Provides a web-based graphical user interface to read biomolecular structures,…

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…

PPD
Dataset

PPD Protein pKa Database

Provides a compendium of protein residue-specific ionization equilibria. The…

Provides a compendium of protein residue-specific ionization equilibria. The PPD serves as a general protein pKa archive and as a source of data that allows for the development and improvement of pKa…

Bluues
Web

Bluues

Calculates numerous electrostatic features including pKa-values and surface…

Calculates numerous electrostatic features including pKa-values and surface potentials. Bluues is a server that uses the program Bluues to perform electrostatic calculations for singleatomic…

PDB_Hydro
Web

PDB_Hydro

Calculates the electrostatic properties of macromolecules which eliminates the…

Calculates the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized…

H++
Web

H++

Automates the process of calculating pKa, protonation states and titration…

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…

Karlsberg+
Web

Karlsberg+

Allows interpreting pK(A)(comp) in terms of pH dependent hydrogen bonding…

Allows interpreting pK(A)(comp) in terms of pH dependent hydrogen bonding pattern and salt bridge geometries. Karlsberg+ is based on numerical solutions of the linearized Poisson-Boltzmann equation…

charge
Desktop

charge

Draws a protein charge plot. charge reads a protein sequence and writes a file…

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…

AcalPred
Web

AcalPred

Provides a useful method for basic academic study and industrial application of…

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…

PHEPS
Web

PHEPS pH-dependent Protein Electrostatics Server

A web service for fast prediction and experiment planning support, as well as…

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…

pKD
Web

pKD

Predicts sets of point mutations that will change the pKa values of a set of…

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…

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