Virtual+Screening

=**Virtual Screening Info:**=

**Directory is called "**LabVS_ZincCBsplitLibrary", NOT "LabVS_CBsplitLibrary"


Use - **PUTTY** that can be run from the Desktop [|putty.exe] (site for this file: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html (Links to an external site.) Download and run it from the desktop
 * PUTTY no workey?**

@http://openbabel.org/wiki/Main_Page
 * Link to Chemical 3-D Minimization Resource**

NOTE: see Tips&Hints page for some other stuff on help with virtual
Are your top hits a PAIN? @http://www.nature.com/news/chemistry-chemical-con-artists-foil-drug-discovery-1.15991?WT.mc_id=TWT_NatureNews

Synopsis of Virtual Techniques (ligand based, structure based) @http://www.dddmag.com/articles/2013/12/new-approaches-virtual-screening

How promiscuous are your top hits? @http://chemutils.florida.scripps.edu:8080/pcpromiscuity/pcpromiscuity.html

Interesting Virtual Screening papers
BCR-ABL - uses MM-PBSA and Docking and MD simulations @http://www.nature.com/srep/2014/141110/srep06948/full/srep06948.html

Docking Flow Center for Structural Genomics of Infectious Diseases (CSGID) @http://link.springer.com/protocol/10.1007/978-1-4939-0354-2_19

Infectious Disease Virtual Screening slide deck

Overview of Virtual Steps @http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644978/

= =
 * Commonly Screened Chemcal Databases** (Cheng et al 2012)
 * PubChem || Public || 30 million || [|http://pubchem.ncbi.nlm.nih.gov] ||
 * ChEMBL || Public || 1 million || [] ||
 * NCI Set || Public || 140,000 || [] ||
 * ChemSpider || Public || 26 million || [|http://www.chemspider.com] ||
 * CoCoCo || Public || 7 million || [] ||
 * TCM || Public || 32,000 || [|http://tcm.cmu.edu.tw] ||
 * ZINC || Public || 13 million || [|http://zinc.docking.org] ||
 * ChemBridge || Commercial || 700,000 || [|http://www.chembridge.com] ||
 * Specs || Commercial || 240,000 || [|http://www.specs.net] ||
 * Asinex || Commercial || 550,000 || [|http://www.asinex.com] ||
 * Enamine || Commercial || 1.7 million || [|http://www.enamine.net] ||
 * Maybridge || Commercial || 56,000 || [|http://www.maybridge.com] ||
 * WOMBAT || Commercial || 263,000 || [|http://www.sunsetmolecular.com] ||
 * ChemDiv || Commercial || 1.5 million || [|http://www.chemdiv.com] ||
 * ChemNavigator || Commercial || 55.3 million || [|http://www.chemnavigator.com] ||
 * ACD || Commercial || 3,870,000 || [] ||
 * MDDR || Commercial || 150,000 || [] ||

***ARCHIVE****
=Virtual Screening info:=

**2017 Stuff**
LigPlot to show what your ligand looks like when docked (in 2-D) European PDB info (EMBL-EBI) @http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1u72&template=ligands.html&l=1.1

Spring 2017 Kelly - DONE
 * First Name || Last Name || Ligand Library || Target Protein ||
 * Nyssa || Berlanga-Barraga || CBZinc1k_100.sdf || YopH ||
 * Alexandra || Boyd || CBZinc1k_101.sdf || EhPTP ||
 * Cormac || Burns || CBZinc1k_102.sdf || EhPTP ||
 * Vivian || Chen || CBZinc1k_103.sdf || YopH ||
 * Irene || Chiang || CBZinc1k_104.sdf || EhPTP ||
 * Edd || Elmir || CBZinc1k_105.sdf || EhPTP ||
 * Stephania || Garcia || CBZinc1k_106.sdf ||  ||
 * Elizabeth || Gray || CBZinc1k_107.sdf || EhPTP ||
 * Sabrina || Guerra || CBZinc1k_108.sdf || EhPTP ||
 * Farrah || Hmaidan || CBZinc1k_109.sdf || EhPTP ||
 * Brian || Ho || CBZinc1k_10.sdf || YopH ||
 * Gabriel || Hoogerbrugge || CBZinc1k_110.sdf || EhPTP ||
 * Marcus || Hunter || CBZinc1k_111.sdf || YopH ||
 * Medha || Iyer || CBZinc1k_112.sdf || YopH ||
 * Limi || Jamma || CBZinc1k_113.sdf || YopH ||
 * Esther || Jimenez || CBZinc1k_114.sdf || EhPTP ||
 * Rosa || Juan || CBZinc1k_115.sdf || EhPTP ||
 * Kaan || Kumru || CBZinc1k_116.sdf || YopH ||
 * Quynh || Lam || CBZinc1k_117.sdf || EhPTP ||
 * Daniel || Lindahl || CBZinc1k_118.sdf || EhPTP ||
 * Ashley || Link || CBZinc1k_119.sdf || EhPTP ||
 * Gina || Liu || CBZinc1k_11.sdf || YopH ||
 * Orlando || Lopez || CBZinc1k_120.sdf ||  ||
 * Ananya || Murthy || CBZinc1k_121.sdf || EhPTP ||
 * Athena || Owirodu || CBZinc1k_122.sdf ||  ||
 * Sung-Hoon || Park || CBZinc1k_123.sdf || EhPTP ||
 * Allison || Petronzio || CBZinc1k_124.sdf || EhPTP ||
 * Yaja || Ramos || CBZinc1k_125.sdf || YopH ||
 * Andre || Ribeiro || CBZinc1k_12.sdf || EhPTP ||
 * Navya || Sankoorikkal || CBZinc1k_13.sdf || YopH ||
 * Jaya || Sigamala || CBZinc1k_14.sdf || YopH ||
 * Todd || Trosclair || CBZinc1k_15.sdf || YopH ||
 * Omar || Vayani || CBZinc1k_16.sdf || YopH ||
 * Cecilia || Williams || CBZinc1k_17.sdf ||  ||
 * Haoyi || Wu || CBZinc1k_18.sdf || YopH ||
 * Tiger || You || CBZinc1k_19.sdf || YopH ||
 * Hannah || Zawatski || CBZinc1k_1.sdf || YopH ||

Use - **PUTTY** that can be run from the Desktop [|putty.exe] (site for this file: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html (Links to an external site.) Download and run it from the desktop
 * PUTTY no workey?**

@http://openbabel.org/wiki/Main_Page
 * Link to Chemical 3-D Minimization Resource**

NOTE: see Tips&Hints page for some other stuff on help with virtual
Are your top hits a PAIN? @http://www.nature.com/news/chemistry-chemical-con-artists-foil-drug-discovery-1.15991?WT.mc_id=TWT_NatureNews

Synopsis of Virtual Techniques (ligand based, structure based) @http://www.dddmag.com/articles/2013/12/new-approaches-virtual-screening

How promiscuous are your top hits? @http://chemutils.florida.scripps.edu:8080/pcpromiscuity/pcpromiscuity.html

Interesting Virtual Screening papers
BCR-ABL - uses MM-PBSA and Docking and MD simulations @http://www.nature.com/srep/2014/141110/srep06948/full/srep06948.html

Docking Flow Center for Structural Genomics of Infectious Diseases (CSGID) @http://link.springer.com/protocol/10.1007/978-1-4939-0354-2_19

Infectious Disease Virtual Screening slide deck

Overview of Virtual Steps @http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644978/


 * Commonly Screened Chemcal Databases** (Cheng et al 2012)
 * PubChem || Public || 30 million || [|http://pubchem.ncbi.nlm.nih.gov] ||
 * ChEMBL || Public || 1 million || [] ||
 * NCI Set || Public || 140,000 || [] ||
 * ChemSpider || Public || 26 million || [|http://www.chemspider.com] ||
 * CoCoCo || Public || 7 million || [] ||
 * TCM || Public || 32,000 || [|http://tcm.cmu.edu.tw] ||
 * ZINC || Public || 13 million || [|http://zinc.docking.org] ||
 * ChemBridge || Commercial || 700,000 || [|http://www.chembridge.com] ||
 * Specs || Commercial || 240,000 || [|http://www.specs.net] ||
 * Asinex || Commercial || 550,000 || [|http://www.asinex.com] ||
 * Enamine || Commercial || 1.7 million || [|http://www.enamine.net] ||
 * Maybridge || Commercial || 56,000 || [|http://www.maybridge.com] ||
 * WOMBAT || Commercial || 263,000 || [|http://www.sunsetmolecular.com] ||
 * ChemDiv || Commercial || 1.5 million || [|http://www.chemdiv.com] ||
 * ChemNavigator || Commercial || 55.3 million || [|http://www.chemnavigator.com] ||
 * ACD || Commercial || 3,870,000 || [] ||
 * MDDR || Commercial || 150,000 || [] ||


 * Spring 2016**
 * First Name || Last Name || Ligand Library || Target Protein ||
 * Safir || Abbas || CB1k_1.sdf || EhPtp ||
 * Jennifer || Agwagom || CB1k_2.sdf || EhPtp ||
 * Mandira || Banik || CB1k_3.sdf || YopH ||
 * Aakash || Barevadia || CB1k_4.sdf || EhPtp ||
 * Morgan || Besmer || CB1k_5.sdf || EhPtp ||
 * Hailey || Cassidy || CB1k_6.sdf || YopH ||
 * Rachel || Clear || CB1k_7.sdf || YopH ||
 * Shadi || Davanloo || CB1k_8.sdf || YopH ||
 * Priya || Guruswamy || CB1k_9.sdf || EhPtp ||
 * Marissa || Hansen || CB1k_10.sdf || YopH ||
 * Akhila || Janapati || CB1k_11.sdf || YopH ||
 * Alexa || Jordan || CB1k_12.sdf || EhPtp ||
 * Areeba || Khwaja || CB1k_13.sdf || YopH ||
 * Justin || Jim || CB1k_14.sdf || YopH ||
 * Gayeong || Lee || CB1k_15.sdf || YopH ||
 * Laura || Luo || CB1k_16.sdf || EhPtp ||
 * Naren || Makkapati || CB1k_17.sdf || YopH ||
 * Paige || Milson || CB1k_18.sdf || EhPtp ||
 * Elisa || Padron || CB1k_19.sdf || EhPtp ||
 * Daniella || Perez || CB1k_20.sdf || YopH ||
 * My || Quan || CB1k_21.sdf || YopH ||
 * Srija || Seenivasan || CB1k_22.sdf || EhPtp ||
 * Maheen || Shakil || CB1k_23.sdf || EhPtp ||
 * Kelly || Sim || CB1k_24.sdf || YopH ||
 * Tarika || Srinivasan || CB1k_25.sdf || EhPtp ||
 * Rachna || Unadkat || CB1k_26.sdf || YopH ||
 * Thomas || Volkman || CB1k_27.sdf || YopH ||
 * Jeremiah || Wells || CB1k_28.sdf || EhPtp ||
 * Amy || Zhou || CB1k_29.sdf || YopH ||

2013 Stuff
100113 - Dr. B has set up some Help Session times for this week See the Google Calendar (link on left hand side of this page) for the times. Location: wet lab (PAI 2.14)

Placing NADPH in your enzyme
Do this if your structure (x-ray or homology model) does not have the NADPH (or NADH) present It should be there for when you are doing your virtual screening (just like when we had NADPH present when we docked against the DHF site of DHFR using MTX as the drug)

In General: In PyMol: download your PDB find another homologous structure in the PDB that has the NADPH present (e.g. your same enzyme in another organism) load this into PyMol in the same session as your protein. Delete any 'extra' chains on your protein or the homologous structure that you don't need (e.g. replicate chains) Align the homologous structure to your structure (don't do the opposite - e.g. aligning yours to the homologous one. This would mess up your coordinates!) See if the NADPH fits into a reasonable place on your protein (does it fit in a pocket) -- if the molecule overlaps with atoms of your protein, then you can 'move' those atoms so that they are not. -- change your mode in PyMol to '3-button editing', left click on an atom you want to move (it should have a gray sphere around it now), Ctrl+Shift+LeftClick on the atom to drag and move it out of the way of the protein atoms. Move the NADPH to a new object Delete the homologous protein (this should leave your NADPH in the PyMol window still) Save the Protein + NADPH as a new, joined PDB file Take this to ICM -- you will use the NAPDH to define your docking site. However, you cannot just use the NADPH in this aligned position from PyMol because it might clash. So, you use ICM to redock it.

From PubChem, download the 3D SDF of NADPH

ICM will need to prep these ligands itself. ........

1st Task
Do homology model if you need to.

Homology Modeling:
if not in PDB, need to make homology model (see Bordoli 2009 Nature Protocols paper), see ICM website Our VDS Homology Model protocol uploaded to GDocs/Protocols/VirtualScreening ProtocolHomologyModelVDS_v4.doc

TIP: for a Homology model, you want to download the 'model' for virtual screening. Don't download the template file for screening.

093013 - an updated, full version is now posted on GDocs/Protocols/VirtualScreeningProtocols:
 * ProtocolVirtualScreenYOURTarget_VDS_Fall13.doc**

2nd Task
Finding a control set of ligands (need about 15 ligands - positive and negative) all members of a Target team do this and compare results

3rd Task
run Lig Prep protocol on your ligands all members of a Target team do this and compare results

4th Task
set up protein for docking all members of a Target team do this and compare results

5th Task
run Control Ligands docking run all members of a Target team do this and compare results

6th Task
run dockings against the Libraries one member of the team will use GOLD other one will use ICM

NOTES - Dr. B 092513 Both people in a pair should independently screen cb306 and compare results - do you get the same thing in general? Then split up and one person does GOLD screening for the other libraries and one person does ICM screening.

2012 STUFF
VETERANS: cb306 should be screened and examined ChembridgeDiversity should be started

and then, when that is done, also screen **CB-kin_UT.sdf ** **Optional: **** HF9PlatesPlates5_9.sdf - ** we have some of these in DMSO in the Robertus Lab **Optional: InHouseCompounds (40 ligands) - **we have these in DMSO in the VDS lab, supposedly.

SPRINGERS: You can go ahead and re-start your run for:**cb306**and then, when that is done, also screen**CB-kin_UT.sdf **

Do NOT screen anything big or it will get bogged down again and no one will get their screening finished.

101512 NOTE: the new version of GOLD (ver. 5.1) uses a new scoring system (PLP). The values of scores is different than what you would have gotten back in the Spring with GOLD Fitness score. @http://beta-www.ccdc.cam.ac.uk/Lists/DocumentationList/gold_release_notes.pdf



From GOLD User Guide v 5.2
The **GOLD fitness function** is made up of four components: • protein-ligand hydrogen bond energy (external H-bond)• protein-ligand van der Waals (vdw) energy (external vdw)• ligand internal vdw energy (internal vdw)• ligand torsional strain energy (internal torsion)• Optionally, a fifth component, ligand in tramolecular hydrogen bond energy (internal H-bond), may be added

The final **ChemScore** value is obtained by adding in a clash penalty and internal torsion terms,which militate against close contacts in docking and poor internal conformations. Covalent and constraint scores may also be included.

@http://biomol.bme.utexas.edu/wiki/index.php/ABS:Flexible_Docking_with_GOLD_and_GLIDE
 * Explanation of GOLD vs. Glide (from Penyu Ren lab at UT engineering)**

@http://biomol.bme.utexas.edu/wiki/index.php/ABS:MM/PBSA_with_amber:_theory_and_application
 * Explanation of MM/PBS (from Pengyu Ren lab at UT engineering)**

NOTE: for the concatenation scripts - use the ones in the **/home/chem204/scripts** folder instead of the one that is in the **VirtualScreenRefresherFiles** -- these will allow you to append your **Bestranking.lst** and **Output.sdf** files correctly.

Blade Rules:

 * only run 1 job at a time
 * only use 6 processors per job

Everyone screens the **HF9PlatesPlates5_9.sdf** library first. Then, after the HF9 library, you want to screen the Chembridge libraries. Screen smallest to Largest.
 * cb-306 only has 306 ligands - so you can do it in one run.

AFTER these two runs - **VERIFY** that the ligands actually dock into the active site (open them up in PyMol with the protein). If they aren't in the right place, you will need to fix something.

Libraries __Available__ (see further below for which ones you will screen).
CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf -rw-r--r-- 1 beckham users 29M Feb 18 2010 ION_Channel3D.sdf -rw-r--r-- 1 beckham users 59M Feb 22 2010 KINASet3d.sdf -rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf -rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf -rw-r--r-- 1 beckham users 860M Feb 22 2010 MicroFormats3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf -rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf -rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf SIGMA -rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf -rw-r--r-- 1 beckham users 3.5M Feb 26 2010 conformersLOPAC_3d.sdf -rw-r--r-- 1 beckham users 6.1M Oct 14 2009 LOPAC_3d.sdf NIH -rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf

2012 Targets
//Leishmania// Target-serine-threonine protein phosphatase (Leishmania major) CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Paul**

MAYBRIDGE -rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one)

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Ling**

MAYBRIDGE -rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Rishi**

//Wolbachia// endosymbiont of //Brugia malayi// Target - 1-deoxy-D-xylulose 5-phosphate reductoisomerase [DXR] (Wolbachia) CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one) NIH -rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf (wait on this one)
 * Urvashi**

MAYBRIDGE -rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
 * Daniel - for DXR**

Target - FabI enoyl-acyl-carrier-protein reductase NADH (Wolbachia) CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf NIH -rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
 * Daniel - for FabI**

//Yersinia// Target - Fab V (Yersinia Pestis)
 * Both screen 3ZU4 and 3ZU5 against your respective libraries**
 * Do the chembridge libraries first,**
 * Then compare your top results and see which compounds do the best.**
 * - make your TopLigands for Chembridge compunds**


 * We will worry about Maybridge after looking at Chembridge results**

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf (wait on this one) -rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one) NIH -rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf (wait on this one)
 * Max**

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf -rw-r--r-- 1 beckham users 860M Feb 22 2010 MicroFormats3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf (wait on this one) SIGMA -rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf (wait on this one)
 * Michael**

Target- Protein Tyrosine Phosphate (Yersinia Enterocolitica) CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Ivy**

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Stephanie**

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Jennifer**

//Francisella tularensis// CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf (wait on this one) -rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one) NIH -rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf (wait on this one)
 * Target -1-deoxy-D-xylulose 5-phosphate reductoisomerase (Francisella Tularensis)**
 * Janice**

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf (wait on this one) -rw-r--r-- 1 beckham users 860M Feb 22 2010 MicroFormats3D.sdf (wait on this one) MAYBRIDGE -rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf SIGMA -rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf (wait on this one)
 * Aldo**

//Trypanosoma brucei// CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Target- Protein Phosphatase 2B**
 * Divya **

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Tom **

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Sajan **

//Plasmodium falciparans// Target - 1-deoxy-D-xylulose-5-phosphate reductoisomerase (P. falciparum) CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf NIH -rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
 * Kaarthik**

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
 * Andrew**

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
 * Alex**
 * use VINA too**

-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf

//Staphylococcus agalactiae -// Neonatal Septicemia Target - S. agalactiae serine-threonine phosphatase STP1 CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Suman **

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Brandon **

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * <span style="font-family: &#39;Calibri&#39;,&#39;sans-serif&#39;; font-size: 14.6667px;">Ruifei **

//Listeria monocytogenes// CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Target - Protein Tyrosine Phosphatase (Listeria monocytogenes)**
 * Akhilesh**

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Mihir**

CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
 * Shane**

//Candida albicans// CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf NIH -rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
 * Target - Methionine Synthase**
 * Priya**

DROPPED TARGETS: Trypanosoma cruzi Target - dihydrofolate reductase-thymidylate synthase (T. cruzi) Alex - use VINA too CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf -rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf NIH -rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf

Ling CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf -rw-r--r-- 1 beckham users 860M Feb 22 2010 MicroFormats3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf SIGMA -rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf

Target - Glyceraldehyde-3-phosphate dehydrogenase (T. cruzi) Andrew CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf -rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf -rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf -rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf NIH -rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf

Rishi CHEMBRIDGE -rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf -rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf MAYBRIDGE -rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf SIGMA -rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf

@VIrtual Screening OLD