Web Tool Links Related to GPCR Study
General Molecular Biology Tools:
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Addgene: https://www.addgene.org
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America Patent: http://www.lens.org/lens/search?n=10&q=6054271&l=en&st=true
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ClusPro: http://cluspro.bu.edu/signup.php
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Degenerate primers design: http://dbmi-icode-01.dbmi.pitt.edu/i-codehop-context/
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DNA sequencing graph: https://digitalworldbiology.com/FinchTV
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EMBLDatabase: http://www.ebi.ac.uk/ena/
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Gnuplot: http://www.gnuplot.info
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KEGG metabolic pathway: https://www.genome.jp/kegg/kegg2.html
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Loop prediction: http://falc-loop.seoklab.org/
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MOL/MOL2: https://sourceforge.net/projects/molmol/
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NMR structure of MP: http://www.drorlist.com/nmr/MPNMR.html
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Oligo Tm Calculator: http://www.basic.northwestern.edu/biotools/OligoCalc.html
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PEP-SiteFinder: http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-SiteFinder/
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Peptide cutsite search: http://web.expasy.org/peptide_cutter/
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Protein-ligand docking: http://www.swissdock.ch/docking# protein-ligand docking
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Pichia genome: http://pichiagenome-ext.boku.ac.at:8080/
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Protease site prediction: http://web.expasy.org/peptide_cutter/
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Protein calculator: http://www.mrc-lmb.cam.ac.uk/ms/methods/proteincalculator.html
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S-S bond analysis tools: http://149.171.101.136/python/disulfideanalysis/search.html
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S-S bond design: http://cptweb.cpt.wayne.edu/DbD2/
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ZINC15 docking: http://zinc15.docking.org
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PyMOL Commands: https://pymol.org/pymol-command-ref.html
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Targeted Drugs: https://pharos.nih.gov/targets
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Interaction Network: http://protein.bio.unipd.it/ring/
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Primer Designing: https://www.agilent.com/store/primerDesignProgram.jsp
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HomoWater: http://lmc.uab.es/homolwat
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DNA tools for space removal http://www.thelabnotebook.com/sequence.php?seq=1
32. Biorender: https://biorender.com
33. MutSig2CV: https://software.broadinstitute.org/cancer/cga/mutsig
NMR and DEER:
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ANM Server: http://gor.bb.iastate.edu/anm/anm.htm
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Basic nmr knowledge: http://chem.ch.huji.ac.il/nmr/techniques/1d/pulseq.htm
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Chemical fluoro: http://www.fluorochem.co.uk/Products/Search
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CPMG online fit software: http://sherekhan.bionmr.org/app/calculation Sherekhan
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CPMG dispersion software: http://home.gna.org/nessy/reference.html
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DEER softwares: http://www.epr.ethz.ch/software
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DEER Simulation Pronox: https://ihlab.hsc.usc.edu/pronox/
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DESMOS WAVE FUNCTION: https://www.desmos.com/calculator
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Library of NMR pulse; http://www.bmrb.wisc.edu/tools/choose_pulse_info.php
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NMR course; http://www.magritek.com/support-videos#01
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NMRviewJ: http://www.onemoonscientific.com/component/users/?view=registration
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Solvent shift and polarity: https://sites.google.com/site/miller00828/in/solvent-polarity-table
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ProShift: http://www.meilerlab.org/index.php/servers/show?s_id=9
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Pulse sequence writing: http://triton.iqfr.csic.es/guide/nmr/smanual/19pul.html
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The nmrPipeFit component: http://pound.med.utoronto.ca/~flemming/fuda/
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The basic NMR: http://www.cis.rit.edu/htbooks/nmr/
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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
24. Protein chemical shift prediction: https://www.protein-nmr.org.uk/general/software/chemical-shift-analysis/
25. NMRFx (spectral processor): https:https://nmrfx.org
26. Ad Bax--pulse sequence: https://spin.niddk.nih.gov/bax/pp/
27. NMR thermodynamics http://chem.ch.huji.ac.il/nmr/software/xsi.htm
Membrane Proteins (GPCR) Tools/Database:
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GPCR database: http://gpcrdb.org/
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GPCR-I-TASSER: https://zhanglab.ccmb.med.umich.edu/GPCR-I-TASSER
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GPCR-SSFE2.0: http://www.ssfa-7tmr.de/ssfe2/precompiled_results_new.php
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GPCR Pharmacology: https://www.guidetopharmacology.org/GRAC/ReceptorFamiliesForward? type=GPCR
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cDNA for GPCRs: https://www.cdna.org/home.php?cat=0
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GPCR-SAS (snakeplot): http://lmc.uab.cat/gpcrsas/gpcrsas/
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GPCR interaction Network: http://www.gpcr-hetnet.com
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MP structural dynamics gateway: http://memprotein.org
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Basic Pharm: http://tmedweb.tulane.edu/pharmwiki