NAD

Background:
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Nicotinamide adenine dinucleotide (NADH) is a ubiquitous redox cofactor that participates in a wide range of enzymatic and regulatory processes. These include metabolism, signalling, and diseases such as cancer and neurodegeneration. Our work presents a comprehensive computational structural analysis of NADH recognition across protein families using 345 NADH-bound crystal structures from the Protein Data Bank. Our study establishes a unified biophysical framework that links NADH shape, interaction signatures, and protein context, providing rational insights for cofactor engineering and the design of NADH-targeted inhibitors.

Content Description:
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This dataset contains: (1) code repository (2) Input datasets
The code repository provides:
(a) Configuration file (/generator/NAIConfig.py)
(b) Code (/generator/NAICofactor.py) for generating statistics around NAI (a three-letter identifier for Nicotinamide adenine dinucleotide in the Protein Data Bank) and its interactions with proteins corresponding to six groups of protein-NAI interaction complexes having six distinct shapes.
Input datasets: (/groups/):
RCSB PDB ids of six different groups of NADH interaction complexes, corresponding to six distinct shapes of the 3-dimensional structures of these complexes

Other Data Used in the Computation:
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(1) RCSB PDB Coordinate files: Retrieved from RCSB PDB (https://www.rcsb.org/)
(2) Protein-Ligand Interaction Profile (PLIP) reports (retrieved programmatically using PLIP utility (https://github.com/pharmai/plip))

Tools and Databases/Resources Used:
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(1) PLIP: PLIP: fully automated protein–ligand interaction profiler - PMC, (n.d.). https://pmc.ncbi.nlm.nih.gov/articles/PMC4489249/#_ad93_
(2) Open Babel: N. M O'Boyle, M. Banck, C. A. James, C. Morley, T. Vandermeersch and G. R. Hutchison, Open Babel: An open chemical toolbox. J Cheminform. 2011 Oct 7;3:33. https://doi.org/10.1186/1758-2946-3-33.
(3) Biopython: P. J. A. Cock, T. Antao, J. T. Chang, B. A. Chapman, C. J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski and M. J. L. de Hoon, Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, Volume 25, Issue 11, June 2009, Pages 1422–1423. https://doi.org/10.1093/bioinformatics/btp163.
(4) Standard Python packages