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





PUTTY no workey?
Use - PUTTY that can be run from the Desktop
putty.exe
View in a new window
View in a new window

(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

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

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
https://www.ebi.ac.uk/chembldb/index.php
NCI Set
Public
140,000
http://dtp.nci.nih.gov/index.html
ChemSpider
Public
26 million
http://www.chemspider.com
CoCoCo
Public
7 million
http://cococo.unimore.it/tiki-index.php
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
http://accelrys.com/products/databases/sourcing/available-chemicals-directory.html
MDDR
Commercial
150,000
http://accelrys.com/products/databases/bioactivity/mddr.html







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.






NOTE: if your jobs don't work - see the Tips & Hints page



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:cb306and then, when that is done, also screenCB-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

GOLD_5dot1_ReleaseNotesScreenshot.JPG

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.

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

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


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)
Paul
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

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

Ling
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

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

Rishi
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







Wolbachia endosymbiont of Brugia malayi
Target - 1-deoxy-D-xylulose 5-phosphate reductoisomerase [DXR] (Wolbachia)
Urvashi
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)

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



Target - FabI enoyl-acyl-carrier-protein reductase NADH (Wolbachia)
Daniel - for FabI
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





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

Max
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)


Michael
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)





Target- Protein Tyrosine Phosphate (Yersinia Enterocolitica)
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
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





Francisella tularensis
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 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)

Aldo
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)





Trypanosoma brucei
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
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







Plasmodium falciparans
Target - 1-deoxy-D-xylulose-5-phosphate reductoisomerase (P. falciparum)
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 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

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
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

-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
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


Ruifei
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







Listeria monocytogenes
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
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






Candida albicans
Target - Methionine Synthase
Priya
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




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