TITLE: Ligand docking using Patchdock for Biochemistry I
AUTHORS: Chris Berndsen

[STEPS]
?. [Docking setup]
Navigate to Patchdock
?. [Docking setup]
In Receptor molecule: Provide your PDB file as a RCSB code OR upload a .PDB file
The receptor molecule is your protein/biomolecule and is generally the larger of the two molecules.
?. [Docking setup]
In Ligand molecule: Provide your PDB file as a RCSB code OR upload a .PDB file.
If you do not have the ligand file, you can create one from information from PubChem and YASARA.
?. [Docking setup]
Under Advanced Options: You can specify a binding site if you have one identified from Uniprot, COACH, BLAST or some other source.
?. [Docking setup]
The binding site location is provided as a .txt file with the following format:88 L89 L90 L91 L92 L93 L95 H96 H101 H102 HThe number indicates the amino acid number, the letter indicates the molecule name in the receptor PDB file (usually A). Note: If the binding site file is not accepted, remove the letters and try again.
?. [Docking setup]
Record your submission settings and add new rows as needed.  AB1Receptor code/file2Ligand code/file3Clustering RMSD
AB1Receptor code/file2Ligand code/file3Clustering RMSD
?. [Docking setup]
Under Clustering RMSD: Set to 1.5 for protein-small molecule binding, 4 for protein-protein or protein-DNA docking.
?. [Docking setup]
Press Submit Form and wait 24 to 72 hours.
?. [Docking setup]
Provide your email address.
?. [Analysis of docking]
Open the results email to go to the table of solutions. This table contains several important pieces of information or files.Solution No: Number of the solutionScore: Geometric shape complementarity score. The more steric clashes the lower the score. The solutions are sorted according to this score.Area: Approximate interface area of the complex.ACE: Atomic contact energy or the energy requried to transfer the molecule from water to protein sitePDB file of the complex: The predicted complex structure in PDB format.
For more about the score see: Duhovny D, Nussinov R, Wolfson HJ. Efficient Unbound Docking of Rigid Molecules. In Gusfield et al., Ed. Proceedings of the 2'nd Workshop on Algorithms in Bioinformatics(WABI) Rome, Italy, Lecture Notes in Computer Science 2452, pp. 185-200, Springer Verlag, 2002For more about the ACE/Atomic contact energy see:Zhang C, Vasmatzis G, Cornette JL, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol. 267(3):707-26, 1997
?. [Analysis of docking]
Record the values for the top 5 hits. Add rows as needed. You can also download the entire solutions table using a link below the table.   ABCD1Solution numberScoreAreaACE23456
ABCD1Solution numberScoreAreaACE23456
?. [Analysis of docking]
Below the table is an option to download the top X hits. Change the number to be between 5 to 10 and obtain the file.
?. [Analysis of docking]
Name the file asproteinname_ligandname_patchdock.zipReplace proteinname with the receptor name, the ligandname with the ligand name.Upload the file to OSF and provide the link to this file as note on this step.
?. [Visualization of docking results]
Extract the .zip file.
?. [Visualization of docking results]
Open all of the hits in a single window of a molecule visualization protein. YASARA will be used in this instance.
?. [Visualization of docking results]
?. [Visualization of docking results]
In the example results in 12.1 most of the solutions cluster in the same area suggesting good complementarity in this region. If not specified before, the list amino acids in this region can be used to specify a receptor site and the docking repeated to refine the placement.
?. [Visualization of docking results]
YASARA users only!With all the solutions loaded, press the space bar to bring up the command window and type the commands shown below. The # indicates explanations that are not typed in the window.# Remove all objects except 1RemoveObj 1# Color protein greyColorRes protein, grey# Select amino acids less than 3 angstroms from the ligand # ligand name. Click on the ligand and look at res name at top rightSelectRes protein with distance # Show, color, and label all amino acids interacting with ligandShowRes selectedColorRes selected, elementLabelRes selected, Format = "RESNAME RESNUM", Height = 1.0, Color = Black, X = 0, Y = 0, Z = 0Remember to replace the ligand name in the SelectRes command with the name of your ligand in YASARA.
?. [Visualization of docking results]
An example result from the commands in Step 14.
?. [Visualization of docking results]
Analyze the amino acids that interact with the ligands and tecord the interacting amino acids using a table with the format below. If desired add tables or rows to the table below to keep results in this protocol.  ABCD1Amino Acid name (Glu, Asp, etc.)Amino acid numberType of weak interactionInteracting group in the ligand23456
ABCD1Amino Acid name (Glu, Asp, etc.)Amino acid numberType of weak interactionInteracting group in the ligand23456
?. [Docking setup]