Repository of Jupyter Notebook and python analysis functions for reproducing study of HIV-1 protease near attack conformation analysis from the papers:

• S.K. Sadiq‡ (2020) Catalysts, Fine-tuning of sequence-specificity by near attack conformations in enzyme-catalyzed peptide hydrolysis, 10 (6) 684
• Sadiq, S.K. ‡ and Coveney P.V. (2015). J Chem Theor Comput. Computing the role of near attack conformations in an enzyme-catalyzed nucleophilic bimolecular reaction. 11 (1), pp 316–324

git clone https://github.com/kashifsadiq/hiv1pr-nacs

The Jupyter notebook: HIV1pr-substrates-NAC-analysis.ipynb contains the analysis script. It imports a python module nac.py, which contains several functions involved in the analysis. The corresponding datasets can be downloaded from Zenodo.

From https://zenodo.org/record/4808575#.YK5MqiaxUlU - download the data.tar file into the directory in which the Jupyter notebook is cloned, then untar it.

tar xvf data.tar

This will create data/apo and data/enz subdirectories containing the apo-substrate and enzyme-substrate systems respectively.