Web Tool Links Related to GPCR Study

General Molecular Biology Tools:

  1. Addgene:                                      https://www.addgene.org

  2. America Patent:                                http://www.lens.org/lens/search?n=10&q=6054271&l=en&st=true

  3. BOXSHADE:                                     http://www.ch.embnet.org/software/BOX_form.html

  4. CLaNP:                                               http://nmr.lic.leidenuniv.nl/paranmr

  5. ClusPro:                                              http://cluspro.bu.edu/signup.php

  6. Degenerate primers design:           http://dbmi-icode-01.dbmi.pitt.edu/i-codehop-context/

  7. DNA sequencing graph:                  https://digitalworldbiology.com/FinchTV

  8. EMBLDatabase:                               http://www.ebi.ac.uk/ena/

  9. Gnuplot:                                             http://www.gnuplot.info

  10. HOLE:                                                http://www.holeprogram.org

  11. KEGG metabolic pathway:             https://www.genome.jp/kegg/kegg2.html

  12. Loop prediction:                               http://falc-loop.seoklab.org/

  13. MOL/MOL2:                                     https://sourceforge.net/projects/molmol/

  14. Naccess:                                             http://www.bioinf.manchester.ac.uk/naccess/

  15. NMR structure of MP:                    http://www.drorlist.com/nmr/MPNMR.html

  16. Oligo Tm Calculator:                       http://www.basic.northwestern.edu/biotools/OligoCalc.html

  17. PEP-SiteFinder:                               http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-SiteFinder/

  18. Peptide cutsite search:                    http://web.expasy.org/peptide_cutter/

  19. Protein-ligand docking:                  http://www.swissdock.ch/docking# protein-ligand docking

  20. Pichia genome:                                 http://pichiagenome-ext.boku.ac.at:8080/

  21. Protease site prediction:                 http://web.expasy.org/peptide_cutter/

  22. Protein calculator:                           http://www.mrc-lmb.cam.ac.uk/ms/methods/proteincalculator.html

  23. S-S bond analysis tools:                  http://149.171.101.136/python/disulfideanalysis/search.html

  24. S-S bond design:                              http://cptweb.cpt.wayne.edu/DbD2/

  25. ZINC15 docking:                              http://zinc15.docking.org

  26. PyMOL Commands:                        https://pymol.org/pymol-command-ref.html

  27. Targeted Drugs:                               https://pharos.nih.gov/targets 

  28. Interaction Network:                      http://protein.bio.unipd.it/ring/ 

  29. Primer Designing:                           https://www.agilent.com/store/primerDesignProgram.jsp

 

NMR and DEER:

  1. ANM Server:                                     http://gor.bb.iastate.edu/anm/anm.htm

  2. Basic nmr knowledge:                     http://chem.ch.huji.ac.il/nmr/techniques/1d/pulseq.htm

  3. Chemical fluoro:                               http://www.fluorochem.co.uk/Products/Search

  4. CPMG online fit software:              http://sherekhan.bionmr.org/app/calculation Sherekhan 

  5. CPMG dispersion software:           http://home.gna.org/nessy/reference.html 

  6. CPMG Lewis Kay’s lab:                   http://code.google.com/p/chemex/ 

  7. DEER softwares:                              http://www.epr.ethz.ch/software

  8. DEER Simulation Pronox:             https://ihlab.hsc.usc.edu/pronox/  

  9. DESMOS  WAVE FUNCTION:     https://www.desmos.com/calculator

  10. Library of NMR pulse;                    http://www.bmrb.wisc.edu/tools/choose_pulse_info.php

  11. NMR course;                                     http://www.magritek.com/support-videos#01 

  12. NMRviewJ:                                       http://www.onemoonscientific.com/component/users/?view=registration

  13. Solvent shift and polarity:              https://sites.google.com/site/miller00828/in/solvent-polarity-table

  14. ProShift:                                             http://www.meilerlab.org/index.php/servers/show?s_id=9

  15. Pulse sequence writing:                  http://triton.iqfr.csic.es/guide/nmr/smanual/19pul.html

  16. The nmrPipeFit component:         http://pound.med.utoronto.ca/~flemming/fuda/

  17. The basic NMR:                                http://www.cis.rit.edu/htbooks/nmr/

  18. Useful links from UC Davis:          https://www.nmr.ucdavis.edu/useful-resources

19.  Protein chemical shifts:                  https://en.wikipedia.org/wiki/Protein_chemical_shift_prediction

20. 1H,13C chemical shift prediction:https://www.nmrdb.org/new_predictor/index.shtml?v=v2.103.0

21. NMR pulse sequence download:   https://nmrfam.wisc.edu/pulse-programs-agilent/

22. A pratical guide: Protein NMR:    https://www.protein-nmr.org.uk/solution-nmr/

23. Chemical shift prediction:             https://fluorine.ch.man.ac.uk/research/p31calc.php

 

Membrane Proteins (GPCR) Tools/Database:

  1. GPCR database:                                 http://gpcrdb.org/

  2. GPCR-I-TASSER:                              https://zhanglab.ccmb.med.umich.edu/GPCR-I-TASSER

  3. GPCR-SSFE2.0:                                 http://www.ssfa-7tmr.de/ssfe2/precompiled_results_new.php

  4. GPCR Pharmacology:                       https://www.guidetopharmacology.org/GRAC/ReceptorFamiliesForward?                                                                    type=GPCR

  5. cDNA for GPCRs:                              https://www.cdna.org/home.php?cat=0

  6. GPCR-SAS (snakeplot):                   http://lmc.uab.cat/gpcrsas/gpcrsas/

  7. GPCR interaction Network:            http://www.gpcr-hetnet.com

  8. MP structural dynamics gateway: http://memprotein.org

  9. Basic Pharm:                                     http://tmedweb.tulane.edu/pharmwiki

©2019 by Libin Ye Lab at University of South Florida

4202 E Fowler Ave, Tampa, FL 33620

Tel: 813-974-6007  E-mail:libinye@usf.edu