ArticlePLoS computational biology2014
Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Two local minima for structures of [4Fe-4S] clusters obtained with density functional theory methods.Scientific reports · 2023Article
- Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase.Molecules (Basel, Switzerland) · 2022Article
- Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins.Inorganic chemistry · 2022Article
- Blending Gagne's Instructional Model with Peyton's Approach to Design an Introductory Bioinformatics Lesson Plan for Medical Students: Proof-of-Concept Study.JMIR medical education · 2018Article
- ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.Journal of chemical information and modeling · 2015Article
- Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design.Journal of chemical information and modeling · 2014Article
- Making biomolecular simulations accessible in the post-Nobel Prize era.PLoS computational biology · 2014Article
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6 authors.
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Abstract
A module for fast determination of reduction potentials, E°, of redox-active proteins has been implemented in the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org). The free energy of reduction, which is proportional to E°, is composed of an intrinsic contribution due to the redox site and an environmental contribution due to the protein and solvent. Here, the intrinsic contribution is selected from a library of pre-calculated density functional theory values for each type of redox site and redox couple, while the environmental contribution is calculated from a crystal structure of the protein using Poisson-Boltzmann continuum electrostatics. An accompanying lesson demonstrates a calculation of E°. In this lesson, an ionizable residue in a [4Fe-4S]-protein that causes a pH-dependent E° is identified, and the E° of a mutant that would test the identification is predicted. This demonstration is valuable to both computational chemistry students and researchers interested in predicting sequence determinants of E° for mutagenesis.
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