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Protonation States

StemSkills Lab > Protonation States

How to Prepare a Protein Structure for MD Simulation (Missing Residues, Hydrogens, Protonation)

10

Jul

Learn to clean a raw PDB for MD: rebuild missing loops, add hydrogens, and fix His, Asp and Cys protonation so your simulation does not crash.

Posted in: Molecular Modeling ,

Tags: GROMACS , Molecular Dynamics , PROPKA , Protein Preparation , Protonation States , Structural Bioinformatics ,

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STEM Skills Lab is a team of scientific experts from diverse backgrounds who have more than a decade of experience in Sequence Bioinformatics, Structural Bioinformatics, Drug Discovery and Designing, Multiscale Modeling of Bio (Chemical) processes, and Modeling of High energy Materials using advanced computational techniques.