Water will find its way: transport through narrow tunnels in hydrolases (water-protein interaction analysis)

<p>Repository including information on the analyses of water-protein interactions by MM/GBSA.</p> <p><strong>hal_mmgbsa_data.tar.gz</strong> - contains a minimal set of files necessary to recreate MM/GBSA calculations and also raw calculation results for Hal.<br><strong>epx_mmgbsa_data.tar.gz</strong> - contains a minimal set of files necessary to recreate MM/GBSA calculations and also raw calculation results for Epx.<br><strong>lip_mmgbsa_data.tar.gz</strong> - contains a minimal set of files necessary to recreate MM/GBSA calculations and also raw calculation results<strong> </strong>for Lip<strong>.</strong></p> <p>In each archive structure is:<br>&nbsp; &nbsp; {supercluster_id}:&nbsp; - supercluster directory<br>&nbsp; &nbsp; &nbsp; &nbsp; {event_nr}_{rounded_radius}:&nbsp; - transport event directory<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; renum.pdb&nbsp; -pdb file containing protein, water of interest and 8 Angstrom radius sphere of surrounding waters<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; water.txt&nbsp; - file denoting water ID for water of interest in the renum.pdb file<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; binding_[implicit|explicit].dat&nbsp; - file containing MMGBSA results for full implicit and partial explicit system<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; decomposition_[implicit|explicit].dat - file containing MMGBSA decomposition results for full implicit and partial explicit system<br>&nbsp; &nbsp; info_{supercluster_id}.csv - file containing descriptions of transport events in supercluster (columns: event_name, radius, frame, simulation, water_id)</p> <p><strong>results.tar.gz </strong>- contains csv files generated by <em>script collect_data_minimal.py</em> for each protein for full implicit and partial explicit solvent. Columns in those csv file are: event_name, supercluster, radius, frame, simulation, water_id, delta_total, delta_van_der_waals, delta_electrostatic, delta_G_solv</p> <p><strong>scripts.tar.gz</strong> - contains following scripts<br>&nbsp; &nbsp; read_transport_events.py<br>&nbsp; &nbsp; prep_inputs.py<br>&nbsp; &nbsp; run_MMGBSA_single.sh<br>&nbsp; &nbsp; collect_data_minimal.py<br>&nbsp; &nbsp; plot_bin.py</p> <p>To recreate MMGBSA calculations with provided inputs one should:<br>$ python read_transport_events.py [Hal.dat|Epx.dat|Lip.dat] &gt; selection.txt<br>Prepare transport events information in a compatible format. Binary transport events databases are available in the repository.</p> <p>$ python prep_inputs.py selection.txt - {absolute output path} {supercluster_id} 1&nbsp;<br>Prepare parm and coordinate file for each supercluster id included in computation. Last argument 1 point script to resume preparations from renum.pdb files.</p> <p>$ bash run_MMGBSA_single.sh {residue_count}<br>Runs MMGBSA for both partial explicit and fully implicit systems. Needs to be run for each event in each supercluster.<br>residue_count should be set to 293 for hal, 319 for epx, and 534 for lip.</p> <p>$ python collect_data_minimal.py [hal|epx|lip]/{supercluster_id} [hal|epx|lip]/info_{supercluster_id}.csv [0|1] &gt;&gt; output.csv<br>Gathers data from MMGBSA calculations for a single supercluster into csv file.&nbsp;<br>Last argument should be 0 for fully implicit system, 1 for partial explicit system.</p> <p>$ python plot_bin.py {hal_implicit_csv} {hal_explicit_csv} {epx_implicit_csv} {epx_explicit_csv} {lip_implicit_csv} {lip_explicit_csv}<br>Results visualization. Produces "combined.png".</p>