Application of CoLD-CoP to Detecting Competitively and Cooperatively Binding Ligands

CompetitiveCooperative_CoLD_CoP_for_archiving.zip will unzip into a directory with two sub-directories. The directory LysozymeNAG has directories with raw data (and NMRPipe format spectra processed in the direct dimension) for DOSYs acquired with a ligands only sample, a ligands + lysozyme sample and a ligands + lysozyme + NAG (N-Acetyl-Glucosamine) sample. This directory also has the key scripts used for DOSY processing and analysis of this dataset. The directory TyrosinaseHCCA similarly has directories with raw data (and NMRPipe format spectra processed in the direct dimension) for DOSYs acquired with a ligands only sample, a ligands + (mushroom) tyrosinase sample and a ligands + tyrosinase + HCCA (4-Hydroxy-a-Cyano-Cinnamic Acid) sample. The TyrosinaseHCCA directory has not only the key scripts used for DOSY processing and analysis of this dataset, but it also has 1D proton spectra acquired on each solution used in this arm of the project. The file das_dosy_nm.m is a customized version of the DOSY processing file used in DOSY processing instead of the dosy_nm.m file used in the DOSY Toolbox. Use of the scripts found in the directories described in the above paragraph requires das_dosy_nm.m as well as NMRPipe, the DOSY Toolbox (https://nmr.chemistry.manchester.ac.uk/?q=node/8), CoLD-CoP toolbox and Covariance Toolbox (both available via MATLAB Central File Exchange). The file lysozyme_complexes_for_docking.zip contains lysozyme structures as minimized in various complexes as well as the ligands from those complexes. These can be used for rescoring or further re-docking, e.g., in FastDRH. DockingAndEnergyMinimization.zip contains some of the files used for docking and energy minimization of the Lysozyme-NAG, Lysozyme-Tris and Lysozyme-GlcNAC complexes.