2021-02-26T18:56:56Z

Yingyang: Created page with "2/25/2021 Ying Yang 1. Train a ML model based on smiles and scores (dock scores / FEP predicted values) 2. Apply the ML model to predict all molecules (smiles) of interest 3..."

2/25/2021 Ying Yang

1. Train a ML model based on smiles and scores (dock scores / FEP predicted values)
2. Apply the ML model to predict all molecules (smiles) of interest
3. Finish analysis of all prediction

2021-02-26T18:48:54Z

Yingyang:

FEP+ for GPCR

2021-02-26T18:48:23Z

Yingyang: Created page with "2/25/2021 Ying Yang Steps for setting up a FEP prediction for membrane protein * Equilibration of complex structure (with confident binding pose) * Force field builder ..."

2/25/2021 Ying Yang

Steps for setting up a FEP prediction for membrane protein

* Equilibration of complex structure (with confident binding pose)
* Force field builder
* Flexible ligand alignment OR core constrain docking
*

DOCK 3.7

2021-02-26T18:32:46Z

Yingyang:

= About =

DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]

DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a
protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.

DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].

{{TOCright}}

= Start here =
* [[So you want to set up a lab]] - only if you don't already have hardware ready.
* [[Install DOCK 3.7]]
* [[Getting started with DOCK 3.7]]
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].
* [[Ligand preparation]] - different version.
* [[Ligand prep Irwin Nov 2016]] - John's current version
* [[Mol2db2 Format 2]] - details on the database formate.
* [[Running docking 3.7]] - how to actually run docking.
* [[DOCK 3.7 Development]] - for software developers
* [[prepare a receptor with a cofactor for docking]]
=== For DOCKovalent, start here ===
* [[DOCKovalent_3.7]]
* [[DOCKovalent lysine inhibitor design tutorial]]
* [[DOCKovalent cysteine inhibitor design tutorial]]

= Tutorials =
'''These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready'''
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)]]
* [[DOCK 3.7 tutorial (Anat)]]
* [[DOCK 3.7 with GIST tutorials]]
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]

= Prepare Receptor =
'''These scripts setup the grids and matching spheres and are used to optimize the pocket'''
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster
* [[Using_thin_spheres_in_DOCK3.7]] - how to add thin spheres directly during blastermaster run (single set of parameters)
* [[How to do parameter scanning]] - how to scan various combinations of low dielectric and ligand desolvation thin spheres without rerunning blastermaster
*[[Matching Sphere Scan]] - how to randomly perturb the matching sphere
*[[Removing Spheres (The Chase Method)]] - removing thin spheres around a specific site in the binding pocket instead of having a continuous layer
* [[Adding Static Waters to the Protein Structure]]
* [[Flexible Docking]]
* [[Visualize docking grids]]
* [[Minimize protein-ligand complex with AMBER]]
* [[Minimize protein-covalent ligand complex with AMBER]]

= Prepare Screening Library =
'''For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building'''
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]
* [[ligand preparation 3.7]]
* [[generating decoys (Reed's way)]]
* [[generating extrema set]]

= Running Docking =
'''These scripts are also out of date. Where is setup_zinc15_file_number.py for LSD?'''
* [[Running docking 3.7]] - JJI currently working on this.
* [[Running DOCK 3.7]] - this seems to be slightly dated.
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.
* Interpreting the [[OUTDOCK 3.7]] file.

= Analysis =
* [[Analyzing DOCK Results]] - this is extract_all.py and getposes.py; not optimized for LSD (i.e. blazing_fast)
* [[How to process results from a large-scale docking]] : contains the blazing fast scripts for LSD processing
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site)
* [[Other Useful Stuff]]
* [[Bootstrap AUC]]
* [[another getposes.py]]
* [[Converting SMILES to Kekule Format]]
* Viewing results using [[ViewDock]]

= Post Docking Clustering=
* [[How to process results from a large-scale docking]]
* [[Large-scale SMILES Requesting and Fingerprints Converting]]
* [[ECFP4 Best First Clustering]]
* [[Bemis-Murcko Scaffold Analysis]]

= Post Docking Filters=
* [[Large-scale TC Calculations]]
* [[Whole Library TC to Knowns Calculations]]
* [[Filtering ligands for novelty]]
* [[Strain Filtering]]
* [[Interaction Filtering]]
* [[Torsion against CSD visualize with Maestro]]

= Redocking with Enhanced Sampling =
*[[Sample Additional Ring Puckers ]]
= Rescoring =
*[[Rescoring_with_DOCK_3.7]]

= Available Libraries =
* [[ZINC Subset DB2 file locations]]
* how to get db2 files from zinc15.docking.org

= Analog by Catalog=
* [[Substructure searching]]
* [[TC analog searching in ZINC]]

= FEP+ and AutoQSAR/DeepChem with Schrodinger Suites=
* [[FEP+ for GPCR]]
* [[AutoQSAR/DeepChem for billions of molecules]]

= Previous verisons and compatibility =
DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],
which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa.

= How to Cite =
To cite the DOCK 3.7 paper, please use
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]

= How to Download =
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].

= How to Setup a Slurm node =
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm

= Implementation =
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].

{{Template:CC-BY-SA-30}}
{{Template:Coleman}}

[[Category:DOCK 3.7]]
[[Category:Software]]
[[Category:Freecom]]

Calculate RMSD between two sets of molecules (eg, Crystal pose vs. docked pose)

2020-10-22T04:30:04Z

Yingyang: Created page with "10/21/2020 Ying Script to calculate RMSD between two sets of molecules (mol2 format), modified from the openeye rmsd.py (https://docs.eyesopen.com/toolkits/python/_downloads/..."

10/21/2020 Ying

Script to calculate RMSD between two sets of molecules (mol2 format), modified from the openeye rmsd.py (https://docs.eyesopen.com/toolkits/python/_downloads/rmsd.py).

To use it, you just need two mol2 files but with match names for the same molecule.

/nfs/home/yingyang/programs/miniconda3/envs/teachopencadd/bin/python \
/nfs/home/yingyang/scripts/rmsd_oe_multi.py -ref <xtal_ligs.mol2> -in <poses.mol2>

* make sure the other conda/python environment is not activated

Other Useful Stuff

2020-10-22T04:22:00Z

Yingyang:

* [[Useful chimera commands]]

* [[calculate volume of the binding site and molecules]]

* [[PDB surface points for figures]]

* [[Analyze ligand geometries using the Cambridge Structural Database (CSD)]]

* [[Calculate RMSD between two sets of molecules (eg, Crystal pose vs. docked pose) ]]

2020-08-05T21:54:08Z

Yingyang:

Interaction Filtering

2020-08-05T21:52:33Z

Yingyang: