Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

H++: a server for estimating pKas and adding missing hydrogens to macromolecules.

John C Gordon1, Jonathan B Myers, Timothy Folta

  • 1Department of Computer Science, Virginia Tech Blacksburg, VA 24061, USA.

Nucleic Acids Research
|June 28, 2005
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Selaginella sellowii gene regulatory networks reveal distinct transcriptional strategies for dehydration stress and recovery.

Scientific reports·2026
Same author

ViraFit: Tunable Fitness Model for Viral Evolution Within a Contact Network.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same author

Comparative genomics of human brain and immune gene preservation across species.

PloS one·2026
Same author

Genomic insights into <i>Ceratobasidium</i> sp. associated with vascular streak dieback of woody ornamentals in the United States using a metagenomic sequencing approach.

Microbiology spectrum·2026
Same author

Reflections on the Presence of Human Cancer Genes in Primate Genomes.

Journal of computational biology : a journal of computational molecular cell biology·2025
Same author

Variant evolution graph: Can we infer how SARS-CoV-2 variants are evolving?

PloS one·2025

This study introduces a web server that simplifies predicting the ionization states of macromolecules. The tool automates complex calculations, providing essential data for biomolecular research and drug design.

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Macromolecular structure and function are influenced by the protonation states of acidic and basic groups.
  • Predicting these protonation states (pK constants) often relies on complex, multi-step calculations using atomic resolution structures.
  • Existing methods can be time-consuming and require significant expertise.

Purpose of the Study:

  • To develop an automated web server for predicting protonation states and related properties of biomolecules.
  • To provide a user-friendly tool for both experts and novices in the field.
  • To streamline the estimation of pK constants, isoelectric points, titration curves, and protonation microstate energies.

Main Methods:

  • Utilizes atomic resolution Protein Data Bank (PDB) structures as input.

Related Experiment Videos

  • Employs continuum electrostatics models for calculations.
  • Automates the process of predicting ionization states and generating output files.

    • Main Results:

    • The web server http://biophysics.cs.vt.edu/H++ provides automated pK predictions.
    • Outputs include pK values, isoelectric points, titration curves, and protonation microstate energies.
    • Generated files are in PQR (Protein Data Bank + charges + radii) format and compatible with AMBER.

    Conclusions:

    • The H++ web server simplifies and accelerates the prediction of biomolecular protonation states.
    • It serves as a valuable tool for researchers in biochemistry, molecular modeling, structural biology, and drug design.
    • The server can also be utilized as an educational resource for biochemistry courses.