ArticleJournal of chemical theory and computation2010
Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF).
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 224 papers.
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Who cites it
224 citing papers in PubMed.
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- Structural basis of Mlc-mediated transcriptional regulation of carbohydrate metabolism.Nature communications · 2026Article
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- Structural insight into hierarchical DNMT3A autoinhibition and its dysregulation in disease.Nature communications · 2026Article
- Chromatin boundary permeability is controlled by CTCF conformational ensembles.bioRxiv : the preprint server for biology · 2026Article
- Mechanistic insights into the noncovalent inhibition of SARS-CoV-2 PLpro: a multiscale computational study.Journal of computer-aided molecular design · 2026Article
- Restoration of the Y220C p53 Full-Length Mutant by PK11000: a Molecular Dynamics Study of an Intrinsically Disordered Protein.ACS omega · 2026Article
- The Allosteric Regulation of the DNA-Binding Domain of p53 by the Intrinsically Disordered C-Terminal Domain.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Identification of a Quinolone-Based Scaffold as a Dual SARS-COV-2 PLᵖʳᵒ and Mᵖʳᵒ Inhibitor: An Integrated Molecular Modeling and In-vitro Evaluation Approach.Drug design, development and therapy · 2026Article
- Mechanistic insights into the selective oxidation of D-arginine by the nonheme iron-dependent viomycin biosynthesis enzyme VioC.iScience · 2025Article
- Dynamical Fragment Molecular Orbital Interaction Analysis of SARS-CoV‑2 RNA-Dependent RNA Polymerase and Remdesivir.ACS omega · 2025Article
164 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Currently the Protein Data Bank (PDB) contains over 18,000 structures that contain a metal ion including Na, Mg, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Cd, Ir, Pt, Au, and Hg. In general, carrying out classical molecular dynamics (MD) simulations of metalloproteins is a convoluted and time consuming process. Herein, we describe MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model (Hoops et al., J. Am. Chem. Soc. 1991, 113, 8262-8270) into the AMBER Force Field (FF). MCPB was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs. The PDB was mined for all Zn containing structures with most being tetrahedrally bound. The most abundant primary shell ligand combinations were extracted and FFs were created. These include Zn bound to CCCC, CCCH, CCHH, CHHH, HHHH, HHHO, HHOO, HOOO, HHHD, and HHDD (O = water and the remaining are 1 letter amino acid codes). Bond and angle force constants and RESP charges were obtained from B3LYP/6-31G* calculations of model structures from the various primary shell combinations. MCPB and ZAFF can be used to create FFs for MD simulations of metalloproteins to study enzyme catalysis, drug design and metalloprotein crystal refinement.
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