Targets

=Perennial Targets= Target - Protein-Tyrosine Phosphatase Yersinia pestis YopH (Bubonic Plague) J.C.

=
Target-protein tyrosine phosphatase (Entamoeba histolytica)....................................Andee F. (Vicky G.) - ARISp16?=====

=NIAID Most Problematic Infectious Diseases= @https://www.niaid.nih.gov/diseases-conditions/infectious-diseases = =

**PART 1:**

 * TDR Targets Searches Exercise (for practice)**

find genes for these criteria using the TDR Targets webpage and then enter them onto spreadsheet:
 * PURPOSE:**
 * **Pick a search, Perform the search, See which targets are found in the list.**
 * **If the target is already on the spreadsheet - __go to the next one that hasn't been entered yet.__**
 * Put your name down in the '**SOURCE / PI**' column for that target and fill in the rest of the information

Phosphatases in T. brucei that have no transmembrane regions, have essentiality evidence, and are druggable at least to 0.5. Phosphatases in T. cruzi that have no transmembrane regions, have essentiality evidence, and are druggable at least to 0.5. Phosphatases in P. falciparum hat have no transmembrane regions, have essentiality evidence, and are druggable at least to 0.5. Phosphatases in P. vivax that have no transmembrane regions, have essentiality evidence, and are druggable at least to 0.5. Phosphatases in T. gondii that have no transmembrane regions, have essentiality evidence, and are druggable at least to 0.5. Phosphatases in M. tuberculosis that have no transmembrane regions, have essentiality evidence, and are druggable at least to 0.5. Phosphatases in L. major that have no transmembrane regions, have essentiality evidence, and are druggable at least to 0.5. Reductase in all (except C. elegans) that have no transmembrane regions, have essentiality evidence, and are druggable at least to 0.6 (be sure to search for reductase and check the box for enzyme)

Spreadsheet for TDR Target Exercise @https://docs.google.com/spreadsheets/d/1b38_yjWxxnQl0rIvuAPXP7HIFcKDf9g_BmlLx9RVGNI/edit?usp=sharing

**PART 2:**
Follow the rest of the Target Discovery Protocol and create a new Wikispaces page that has all the info you need for a target. (the Wikispaces page will link from here)
 * SELECTING YOUR TARGET**
 * NOTE:** do this ONLY after you have completed the above TDR Targets exercise.

**H**ow To Create a New Target page
Login to Wikispaces, Edit __this__ Targets page with a title that will link to your __new__ page, Type a new line that says : While still in the editing mode, Highlight the first part of what you just typed (e.g. the part without your name), Click on the 'Link' button above on the toolbar, Click ' **New Window**' under Page or File, Click '**Add Link**' -- This will create a new page. -- Save the current page -- Click on the link to your new page. It will say "This page doesn't exist yet. You can create it by clicking the edit button" -- Edit the page by copying and pasting the '**Format for Individual Target pages**' shown below. Then fill in the respective information for each item....

*NOTE; Do not use "/" in your page titles Genus and species name should be in //italics//

"Target -  ................"

**Spring 2018 Target Selection Pages**
ENTER THE LINKS TO YOUR TARGET PAGES HERE
 * For Example: **

=
TargetSp18- Thymine Diphosphate-Glucose 4,6 dehydratase (//Bacillus anthracis)//.............................................................................................................Taylor G.===== TargetSp18 - Glycerol-3-Phosphate Dehydrogenase (//Leishmania Mexicana).............................................................................................................................//Erina L. TargetSp18 - GlcB malate synthase, Mycobacterium leprae ..............................................................................................................................................................................Remya N. TargetSp18 - Dihydrofolate Reductase (//Bacillus anthracis//).......................................................................................................................................................Salma G. TargetSp18 - Dihydrofolate Reductase //Klebsiella pneumoniae//......................................................................................................................................................Joe Y. TargetSp18 - Probable Adenylate Kinase ADK (//Mycobacterium tuberculosis)//.............................................................................................................................Safir A. TargetSp18 - Trypanosoma Brucei dihydroorotate oxidase.............................................................................................................................................HaoTing Huang TargetSp18 - Bifunctional N-acetylglucosamine-1-phosphate uridyl transferase (GlmU) //Mycobacterium tuberculosis//.......................................................... Megan Vu TargetSp18 - Beta-lactamase A, Yersinia enterocolitica...........................................................................................................................................................Anthony Z. TargetSp18 - Catalase-peroxidase Mycobacterium tuberculosis............................................................................................................................................... Inaara S. TargetSp18 - Nucleoside Diphosphate Kinase //Acinetobacter baumannii.......................................................................................................................................//Mai D. TargetSp18 - Alkaline metalloproteinase, //(Pseudomonas aeruginosa////)//.....................................................................................................................................Kelly K. TargetSp18 - Enterotoxin C3 (SEC 3), Staphylococcus aureus...............................................................................................................................................Pareesa H. TargetSp18 - Carbamate Kinase, Giardia Lamblia//..............................................................................................................................................................//Travis Woods TargetSp18 - Zinc metalloproteinase, Bacillus anthracis..............................................................................................................................................................Marie P. TargetSp18 - Exo-alpha-sialidase - Influenza A Virus..............................................................................................................................................................Michelle G. TargetSp18 - Glyceraldehyde-3-phosphate Dehydrogenase //(Bacillus anthracis)//..................................................................................................................... Aslinur O. TargetSp18 - Dihydropteroate synthase TYPE 2 //Mycobacterium tuberculosis (strain ATCC 25618/ H37Rv)//..............................................................Colby Buckhanan TargetSp18 - @Octameric Enolase (Streptococcus pneumoniae)//..................................................................................................................................////...............// Moses A. TargerSp18 - Ecto-ATPase //(Balamuthia mandrillaris)//..................................................................................................................................................................Taylor S. TargetSp18 - Hypoxanthine guanine phosphoribosyltransferase //(////Mycobacterium tuberbulosis)//..................................................................................................Marie L. TargetSp18 - Probable cation-transporter ATPase I CtpI, //Mycobacterium tuberculosis.//.....................................................................................................Sanna Jawaid TargetSp18 - UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopi melate-D-alanyl-D-alanyl ligase //Mycobacterium tuberculosis(H37Rv)//.......................Anibeth C. TargetSp18 - ATP:protein-L-histidine N-phosphotransferase, //Mycobacterium tuberculosis////.....................................................................................................Eduardo C.// TargetSp18 - Dihydropteroate synthase //Mycobacterium Leprae// ..................................................................... Sue Jin P. TargetSp18- @Thioredoxin reductase (NADPH) Myobacterium Bovis.........................................................................................................................................Kellen R. TargetSp 18 - KatE catalase //Leptospira interrograns................................................................................................................................................................//Samuel O.

=
TargetSp18- Phosphoglycerate kinase A (//Crithidia fasciculata//)...................................................................................................................................................Sadiat A.====== TargetSp18- GMP Synthase //Methanocaldococcus jannaschii// ..................................................................................................................................................Lauren Y.

=
TargetSp18 - Lactate dehydogenase (//Cryptosporidium parvum//)..............................................................................................................................................Jacky X.====== TargetSp18 - @Dengue Methyltransferase........................................................................................................................................................................................Tom S.

=
TargetSp18- Lysyl tRNA Synthetase (////Mycobacterium ulcerans////).............................................................................................................Tyler G. ===== =Summer 2017 Target Discovery= = =

Revivals
TargetF15 - S-adenosylmethionine Synthetase (Mycobacterium tuberuclosis)....................................Bethany R., Ana R. **Su17 - Alexandra B, Haoyi W, Marcus H.** TargetF15 - D-alanine Ligase (Listeria monocytogenes).....................................................................Simone M. **Su17 - Edd E., Esther J.,** TargetF15 - 6-phosphoglucanate dehydrogenase, decarboxylating, putative (Trypanosoma cruzi)...Diane C. **Su17 - Kaan K, Sung-Hoon P,**
 * Not Cloned Yet**

TargetF15- 6-phosphogluconate dehydrogenase, decarboxylating, putative (Leishmania major)....Mayur P. TargetF15 - S-adenosylmethionine Synthetase (Burkholderia pseudomallei)......................................Matthew N., Justin H.


 * Target - Protein Tyrosine Phosphatase (Listeria monocytogenes) ---** Akhilesh, Mihir, Shane **Fall17 - Irene C, Farrah H, Medha, Gina L.**

Target - PP2C- Ser Thr Phosphatase (//Mycobacterium tuberculosis)//............ **Fall17 - Nyssa BB, Gabriel H, Navya S, Cormac B,**

Target - Inogranic pyrophosphatase (//Burkholderia pseudomallei) ..............................// **Fall17 -Vivian C, Jaya S, Athena O, Daniel L, Todd**

D-alanine ligase (Yersinia pestis)........................................................................................**Su17 - Rosa J, Allison P,** 6-phosphoglucanate dehydrogenase ( //T. gondii//)................................................................... **Su17 - Quynh (Megan) L, Shaochen (Tiger) Y**
 * New**

D-alanine ligase (//K. pneumoniae//)......................................................................................... not enough info for a target 6-phosphoglucanate dehydrogenase ( //L. monocytogenes//)...................................................- Not enough info on essentiality
 * Not used**


 * Target -1-deoxy-D-xylulose 5-phosphate reductoisomerase (Francisella Tularensis)--**Janice, Aldo
 * @TargetSp17- PP2C- family Ser Thr Phosphatase (Mycobacterium tuberculosis)...Cecilia Williams - good - Dr .B
 * @TargetSp17 - Inogranic pyrophosphatase (Burkholderia pseudomallei) . . . . . Vivian C. good Dr. B

TargetSp17 - NH 3 -dependent NAD synthetase (Clostridium botulinum)....Brian H. - good Dr B - No, is an Octamer. - DR. B

http://www.rcsb.org/pdb/explore/explore.do?structureId=5BPF

RpFabG - Aparna Geovanny - EhPTP & 6-phosphoglucanate dehydrogenase (P. vivax) Tu - KPC-2 & ? Lizzie - MtDalaDala Nura - EhPTP & ??
 * ARI**

Possibles for **ARI** (cloned into vector already): Target - 6-phosphoglucanate dehydrogenase (P. vivax).............................................Nikki W., Carolyn T, __ARI-Sp16__: Cindy N. Target- 6-phosphogluconate dehydrogenase (T. brucei) .............................................................(Created by Emily J.) Researchers: Kavya K. and Vicky G. __ARI-Sp16__: Sam D. Target - 1-deoxy-D-xylulose-5-phosphate reductoisomerase (P. falciparum)-Kaarthik, **Andrew, Alex** IMP-7: (metal-dependent), pET-28b, His Tag

=Spring & Summer 2017 Target Selection Pages=


 * New Targets:**
 * TargetSummer17 -
 * Good:**
 * TargetSp17 - Biotin carboxylase (Staphylococcus aureus).....Tiger Y. - may work if we can just measure BC activity vs ACC activity as a whole - DR. B - Assay is coupled - Dr. B
 * TargetSp17 - Biotin carboxylase (Staphylococcus aureus).....Tiger Y. - may work if we can just measure BC activity vs ACC activity as a whole - DR. B - Assay is coupled - Dr. B


 * TargetSp17-fabH 3-oxoacyl-[acyl-carrier-protein] synthase 3 ( //Francisella tularensis//).........Marcus H. (what is the PDB for this? - DR. B)
 * @TargetSummer17 - 3D7, ribonucleotide reductase small subunit (P.falciparum).......Lizzie Gray (Haoyi Wu)
 * From TDR targets exercise:
 * serine-threonine protein phosphatase catalytic subunit, putative... Marcus H.
 * @3D7 ribonucleotide reductase small subunit... Lizzie G.
 * TargetSummer17 - EhPTP, low molecular weight protein tyrosine phosphatase// (Entamoeba histolytica)// . . . . . Kian C.
 * TargetSummer17 - EhPTP, low molecular weight protein tyrosine phosphatase// (Entamoeba histolytica)// . . . . . Kian C.


 * Okay:**
 * TargetSp17 - DNA polymerase alpha, positive (//Plasmodium vivax//)...... Alexandra B.
 * TargetSp17- type II site-specific deoxyribonuclease(Escherichia coli) .....Esther J.
 * TargetSp17 - FlaA flagellar outer sheath protein (Leptospira Interrogans).....Daniel L.
 * TargetSp17- Pyruvate kinase, putative (//Toxoplasma gondii//).... Ezzeddine E.
 * TargetSp17- Phophoglycerate Kinase (//Mycobacterium tuberculosis//).....Ashley L.
 * TargetSp17- DNA-directed RNA polymerase III subunit (Plasmodium vivax)....Farrah H.
 * TargetSp17 - Thymidylate synthase (//Neisseria gonorrhoeae//).....Nyssa B.
 * TargetSp17- Wall Teichoic Acid beta-glycosyltransferase tarS (Staphylococcus aureus).....Todd T.
 * @TargetSp17 - NADH ubiquinone reductase Na ion transporting (Vibrio cholerae)......Haoyi W.
 * TargetSp17 - N-acylmannosamine kinase (//Streptococcus pneumoniae//) - Allison Petronzio
 * @TargetSp17 - S-adenosylmethionine syntheses (Coxiella burnetii)...Limi J.
 * @Target Sp17 - Alkaline Phosphatase (Clostridium botulinum)...... Athena O.
 * @TargetSp17 - Dihydrofolate Synthase (Mycobacterium leprae) ...... Rosa J.
 * TargetSp17 - Dihydropteroate synthase (S. enteritidis)....Medha I. -Substrates not readily available - Dr. B 060617
 * TargetSp17 - Nitric-oxide synthase (Bacillus anthracis)......Sabrina G. - Complicated assay - Dr. B 0606017
 * TargetSp17 - Protein serine/threonine phosphatase //(Trypanosoma brucei)////......// Ananya M. - Done before - Dr. B
 * TargetSp17 - FabI enoyl-acyl carrier protein reductase (//Francisella tularensis).....// Omar V. - expensive substrates - Dr. B
 * TargetSummer17 - Serine Threonine protein phosphatase 2B catalytic subunit A2, putative (T. cruzi)- ....... Ezzeddine Elmir (Haoyi Wu) - Done before - Dr. B
 * @TargetSp17- ATP- dependent Clp protease proteolytic subunit..... Kaan K. - Enzyme assay do-able, but involved. ** - ** is this functional as a monomer?? - NO. Dr. B


 * Bad:**
 * =====Trypanosome cruz, calpaan like cysteine peptidase, putative ... Hannah Zawatski=====
 * @TargetSp17 - Adenylate kinase (T. Brucei)..... Sung-Hoon P.
 * @TargetSp17 - Ricin Toxin Chain A & B (Ricinus communis) . . . Cormac B.
 * TargetSp17- Ser_Thr Protein Kinase B PKNB (//Mycobacterium Canettii)......//Navya S.
 * TargetSp17- protein phosphatase type 1, putative (S. mansoni)........Quynh L.
 * TargetSp17-phosphatidylinositol 4-kinase, putative(//Plasmodium vivax//)......Gina L. //
 * TargetSummer17 - AMP deaminase, putative (//P. falciparum//)........ Alexandra B.

TargetSp16- 6-phosphogluconate dehydrogenase, decarboxylating, putative //Leishmania major// ..............Laura L., Naren M TargetSp16- 6-phosphogluconate dehydrogenase, decarboxylating, putative //T. cruzi..//........... Bella, Elisa P TargetSp16- S-adenosylmethionine Synthetase //Mycobacterium tuberculosis// ....................Aakash B., Kelly S, Priya G (Summ17) TargetSp16- Tyrosine-protein phosphatase CpsB (//Streptococcus pneumoniae)// ...........Justin Kim, Rachel C TargetSp16- Low Molecular Weight Phosphotyrosine phosphatase (//Vibrio Cholerae)// ......Hailey C., Tommy V

= Fall 2016 Targets = TargetSp16- 6-phosphogluconate dehydrogenase, decarboxylating, putative //Leishmania major// ..............Laura L., Naren M TargetSp16- 6-phosphogluconate dehydrogenase, decarboxylating, putative //T. cruzi..//........... Bella, Elisa P TargetSp16- Glutathione reductase (Plasmodium falciparum 3D7)//.//.............Jennifer A, Gayeong TargetSp16- D-alanine ligase //Listeria monocytogenes// ............Amy Z, Akhila J, Josue TargetSp16- S-adenosylmethionine synthetase //Burkholderia pseudomallei// ........... ??????? TargetSp16- N-acetylneuraminic acid synthase (//Neisseria meningitidis)////........//My Q., Shadi TargetSp16- S-adenosylmethionine Synthetase //Mycobacterium tuberculosis// ....................Aakash B., Kelly S PriyaG? TargetSp16- Tyrosine-protein phosphatase CpsB (//Streptococcus pneumoniae)// ...........Justin Kim, Rachel C TargetSp16- Low Molecular Weight Phosphotyrosine phosphatase (//Vibrio Cholerae)// ......Hailey C., Tommy V

TargetSp16- (FlaB)(Lyme borreliosis). . . .Jeremiah W. TargetSp16 -@sipD (Salmonella invasion protein D) Salmonella typhimurium //....// Kelly S//.// TargetSp16 - Glucose-6-phosphate dehydrogenase //(Plasmodium falciparum).................// Paige M//.// TargetSp16 - Beta lactamase class A (//staphylococcus aureus//) ...........................Maheen S. TargetSp16- GuaA (//Borrelia burgodorferi). . . .//Mandy B. Target Sp16- AEK1 (//Trypanosoma brucei//).........Shadi D. Target Sp16-manganese-dependent inorganic pyrophosphatase (Streptococcus agalactiae)....Elisa P. Target Sp16- Glutathione reductase (Plasmodium falciparum 3D7)....................Jennifer A. TargetSp16- TbPIP5K1 (phosphatidylinositol 4-phosphate 5-kinase) //Trypanosoma brucei...............//Tarika S. TargetSp16-Microcin C7 self-immunity protein MccF (Bacillus anthracis).........Daniella Perez TargetSp16- Ribosomal RNA Large Subunit Methyltransferase Cfr (//Clostridium botulinum//) ..........Tommy V.

TargetSp16- @4-(cytidine 5' -diphospho)-2-C-methyl-D-erythritol kinase (Bacillus anthracis)..................Areeba K. TargetSp16- 5-O-(1-carboxyvinyl)-3-phosphoshikimate phosphate-lyase (Campylobacter jejuni)........Aakash B. TargetSp16- @Thioredoxin Reductase (Entamoeba Hystolica) ........ Marissa H. TargetF15- @phospholipase C (clostridium perfrigens).......................................Gayeong L.

TargetSp16- Shiga Toxin subunit B (//Shigella dysenteriae//).............Amy Z. TargetSp16- Clostripain (Clostridium botulinum) ............Rachel C. TargetSp16- Fb G 3-ketoacyl-(acyl-carrier-protein) reductase...........Rachna U.

TargetSp16- @Serine-threonine protein kinase PknG (Mycobacterium leprae) ................Laura L

= ARI Targets (Sp16) = TargetF15 - Klebsiella Pneumoniae Carbapenamase-2 (Klebsiella pneumoniae..............................Jeffrey X. TargetF15 - Verona-integron encoded Metallo-beta Lactamase (Pseudomonas aeruginosa)............Steven T. Target - D-alanine:D-alanine Ligase. (M. tuberculosis)..............................................., Chris T. Charina B (VDS, ARI-Sp16) Target - 6-phosphoglucanate dehydrogenase (P. vivax).............................................Nikki W., Carolyn T, __ARI-Sp16__: Cindy N. Target- 6-phosphogluconate dehydrogenase (T. brucei) .............................................................(Created by Emily J.) Researchers: Kavya K. and Vicky G. __ARI-Sp16__: Sam D.

TargetSp13 - Fab G 3-ketoacyl-(acyl-carrier-protein) reductase .( Rickettsia prowazekii )................................**RpFabG**..........................Researchers: Priya P. Oscar V Betty H - - __ARISp16__ Ramiro, Aparna
 * POSSIBLES**:

Target - FabG 3-oxoacyl-(acyl-carrier protein) reductase (P. falciparum) .......................... Researchers: Melissa H. & Jason P. - __ARISp16__: - Nishtha

Target - 3-oxoacyl- (acyl-carrier-protein) reductase (Mycobacterium tuberculosis) ............ (Created by Caroline C) Researcher: Grace & Young - __ARISp16__ - Rayudu

=
Target-protein tyrosine phosphatase (Entamoeba histolytica).......................**EhPTP**.............Andee F. (Vicky G.) - __ARISp16:__ Timothy, Brian=====


 * NDM-1** http://vdsstream.wikispaces.com/NDM-1+Beta-lactamase+Project ....................... __ARISp16:__ Kyle, Sonia, Sarah, Sabi

++++++++++++++++++++++++++++++++++++++++++++++++++++++

Format for Individual Target pages (copy this list to new Target page and then fill in for your target):
Is it a monomer or multimer as biological unit**? (make prediction at** @http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html):
 * Target (protein/gene name):**
 * NCBI Gene # or RefSeq#:**
 * Protein ID (NP or XP #) or Wolbachia#:**
 * Organism (including strain):**
 * Etiologic Risk Group (see link below):**
 * /  Disease Information   (sort of like the Intro to your Mini <span style="background-color: transparent !important; border-image: none !important !important; border: currentColor !important; display: inline-block !important; float: none !important; font-size-adjust: none !important; font-stretch: normal !important; font: bold 13.33px/26px arial,helvetica,sans-serif !important; height: auto !important; margin: 0px !important; min-height: 0px !important; min-width: 0px !important; padding: 0px !important; text-decoration: underline !important; vertical-align: baseline !important; width: auto !important;">Research Write up):**
 * Link to TDR Targets page (if present):**
 * Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)**
 * Essentiality of this protein:**
 * Complex of proteins?:**
 * Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):**


 * *EC#: **
 * Link to BRENDA EC# page:**
 * --** Show screenshot of BRENDA enzyme mechanism schematic
 * Enzyme Assay  information (spectrophotometric, coupled assay ?, reagents):**
 * -- link to Sigma (or other company  ) page for assay (see Sigma links below)**
 * -- -or link (or citation) to paper that contains assay information**
 * -- links to assay reagents (substrates) pages.**
 * --- List cost and quantity of substrate reagents, supplier, and catalog #**

-- PDB # or closest PDB entry if using homology model: -- For Homology Model option: Show pairwise alignment of your BLASTP search in NCBI against the PDB Query Coverage: Max % Identities: % Positives Chain used for homology:
 * Structure (PDB or Homology model)**


 * Current Inhibitors:**
 * Expression Information (has it been expressed in bacterial cells):**
 * Purification Method  :**
 * Image of protein (PyMol with features delineated and shown separately):**
 * Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):**
 * length of your protein in Amino Acids**
 * Molecular Weight  of your protein in kiloDaltons using the [|Expasy ProtParam] website**
 * Molar  Extinction coefficient   of your protein at 280 nm wavelength:**
 * TMpred graph Image ** (@http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
 * CDS  Gene Sequence   (paste as text only):**
 * GC% Content for gene:**
 * CDS Gene Sequence (codon optimized) - copy from  output   of   Primer Design   Protocol (paste as text only):**
 * GC% Content for gene (codon optimized):**

Do Not Need this info for Spring  (but still copy these lines to your Target page for now) -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
 * Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):**
 * ( link to DNA Works output  text file   - **that should be saved in your   Google Docs   folder after you did the primer design protocol)


 * Primer design results for 'tail' primers (this is just 2 sequences):**

RESOURCES:
See **ProtocolTargetDiscoveryVDS.docx** for more Etiologic Risk Group Categories (for pathogens): http://www.utexas.edu/research/rsc/ibc/agent_class.html#_Toc7238334

UT Libraries Page on BIOCHEMISTRY: @http://guides.lib.utexas.edu/c.php?g=498744&p=3414807

PlasmoDB: @http://plasmodb.org/plasmo/ EuPathDB: @http://eupathdb.org/eupathdb/ EnsemblProtists: @http://protists.ensembl.org/index.html GeneDB: @http://www.genedb.org/Homepage Sanger Centre Plasmodium Genome Projects: @http://www.sanger.ac.uk/Projects/P_falciparum/ Medicines for Malaria Ventures: http://www.mmv.org Drugs for Neglected Diseases Initiative: @http://www.dndi.org/ The Bill and Melinda Gates Foundation @http://www.gatesfoundation.org/Pages/home.aspx St. Jude Children's Research Hospital: http://www.stjuderesearch.org Novartis Institute Tropical Disease: @http://www.novartis.com/research/nitd/index.shtml TDR Targets: http://www.tdrtargets.org ChEMBLdb: @http://www.ebi.ac.uk/chembldb ChEMBL Blog: @http://chembl.blogspot.com/ ChEMBL NTD (neglected tropical diseases): @https://www.ebi.ac.uk/chemblntd

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

To find homologous structures - go into the PDB and do an Advanced Search. One of the options on the pull down window on the Advanced Search page is Enzyme Classification. Type in your EC number. It will give you a list - then narrow that down on the left hand side by other bacterial/protozoan organisms (pick ones that are more taxonomically similar to your organism) NOTE: this just finds homologous enzymes - but these may not be sufficient for creating a homology model. Need to do BLAST pairwise comparison to determine that.
 * Finding Homologous Structures of your protein in the PDB**

Enzyme Explorer @http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer.html
 * SIGMA-ALDRICH RESOURCES**

Enzyme Classification Index (EC number) @http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=14573088

Enzyme Explorer Assay Library - has the awesome assays. @http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/learning-center/assay-library.html

WolframAlpha @http://www.wolframalpha.com/ DrugBank @http://www.drugbank.ca/

@http://www.niaid.nih.gov/Pages/default.aspx @http://eupathdb.org/eupathdb/ @https://patricbrc.vbi.vt.edu/portal/portal/patric/Home @http://www.nmpdr.org/FIG/wiki/view.cgi/Main/EssentialGenes @http://tubic.tju.edu.cn/deg/ @http://csgid.org/csgid/cake/pages/community_request_gateway @http://tdrtargets.org/ @http://gsc.jcvi.org/status.shtml
 * Databases of genes/organisms:**

@http://wwwnc.cdc.gov/eid/pages/scientific-nomenclature.htm
 * Scientific Nomenclature page from  Center for Disease   Control (gene, protein names and abbreviations)**

NCBI GENE Page: @http://www.ncbi.nlm.nih.gov/gene BLAST Page: @http://blast.ncbi.nlm.nih.gov/
 * Gene Information:**

NCBI Protein Page: @http://www.ncbi.nlm.nih.gov/protein Protein Expression Website Protein Expression  Paper:
 * Protein Information:**


 * Primer Overlap PCR Articles**


 * Is my target good for Virtual Screening programs?**

UT Libraries Pages
Biomedical Big Data Resource Center Biochemistry (Bioinformatics and Cheminformatics Tools)

Dr. B
Link to other page filarial target Wolbachia target protozon (A, B, C) list:
 * Cryptosporidium parvum
 * Cyclospora cayatanensis
 * Giardia lamblia
 * Entamoeba histolytica
 * Toxoplasma

@White nose bat disease

Anaplasma, Babesia, Bartonella, Borrelia, Brucella, Burkholderia, Coccidioides, Cryptosporidium, Ehrlichia, Encephalitozoon, Entamoeba, Giardia, Mycobacterium, Rickettsia, Salmonella
 * Seattle Structural Genomics Targets** - see my Targets folder.

<span style="background-color: transparent; color: #000000; display: block; font-family: arial; font-size: 11pt; font-style: normal; font-weight: normal; height: 1px; left: -10000px; overflow: hidden; position: absolute; top: 706px; vertical-align: baseline; width: 1px;">ACGCTGGTCGACGAAGGCCGGATCACCCCGGAGGAGGCGCACAGCCACCCGCAACGCTCGTTGATCATGCGGGCGTTGACCGGCCATGAGGTCGAACCGACGCTGACCATGCGAGAAGCCCGCGCCGGTGATCGTTACCTGCTGTGCTCGGACGGGTTGTCCGATCCGGTTAGCGATGAAACTATCCTCGAGGCCCTGCAGATCCCCGAGGTTGCCGAGAGCGCTCACCGCCTCATTGAACTGGCGCTGCGCGGCGGCGGCCCCGACAACGTCACTGTCGTCGTCGCCGACGTCGTCGACTACGACTACGGCCAGACCCAACCGATTCTGGCCGGGGCGGTCTCAGGCGACGACGACCAACTGACCCTGCCCAACACCGCCGCCGGCCGGGCCTCTGCCATCAGCCAGCGCAAGGAGATCGTTAAACGCGTTCCGCCACAGGCCGATACATTCAGTCGGCCACGGTGGTCGGGCCGACGGCTAGCATTCGTTGTCGCACTGGTGACCGTGCTGATGACTGCGGGCCTGCTCATTGGTCGCGCGATCATCCGCAGCAACTACTACGTAGCGGACTACGCCGGCAGCGTGTCCATCATGCGGGGGATTCAAGGGTCGCTACTGGGCATGTCCCTGCACCAGCCTTACCTGATGGGCTGCCTCAGCCCGCGTAACGAGCTGTCGCAGATCAGCTACGGACAGTCTGGGGGCCCTCTCGACTGCCATCTGATGAAACTGGAGGATCTGCGACCGCCGGAGCGCGCACAGGTTCGGGCCGGTCTCCCGGCCGGCACTCTCGATGACGCCATCGGGCAGTTGCGCGAACTGGCGGCCAACTCCCTG <span style="background-color: transparent; color: #000000; display: block; font-family: arial; font-size: 11pt; font-style: normal; font-weight: normal; height: 1px; left: -10000px; overflow: hidden; position: absolute; top: 706px; vertical-align: baseline; width: 1px;">CTGCCGCCTTGCCCGGCGCCGCGTGCCACGTCCCCGCCCGGGCGCCCGGCCCCACCCACCACCAGCGAGACAACCGAACCAAACGTCACCTCCTCGCCAGCCTCTCCATCACCCACCACCTCCGCGCCGGCCCCCACCGGAACTACTCCTGCCATCCCCACGAGTGCCTCCCCGGCAGCGCCCGCGTCGCCGCCGACGCCTTGGCCCGTCACCAGCTCGCCGACGATGGCCGCACTTCCGCCACCCCCGCCTCAGCCGGGCATCGACTGCCGGGCGGCGGCATGA

<span style="display: block; height: 1px; left: -10000px; overflow: hidden; position: absolute; top: 5950px; width: 1px;">|| <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 13461px; width: 1px;">1-deoxy-D-xylulose-5-phosphate reductoisomerase <span style="display: block; height: 1px; left: 0px; overflow: hidden; position: absolute; top: 5798.5px; width: 1px;"><span style="display: block; height: 1px; left: 0px; overflow: hidden; position: absolute; top: 5798.5px; width: 1px;">Gene Symbol <span style="display: block; height: 1px; left: 0px; overflow: hidden; position: absolute; top: 6076.5px; width: 1px;">alkaline phosphatase