I am looking for a reliable web site which I can give chemical name or molecular formula of compounds and software can identify the target proteins.
Try to use PASS online-way2drug. Registration and use is free and available at; http://www.pharmaexpert.ru/passonline/
ChEMBL! You can even design the molecule and find other compoounds with similar structure and targets; reverse queries (target -> compounds) are also possible. No registration needed and very user friendly.
https://www.ebi.ac.uk/chembl/
Yes CheMBL is good one database but you may found below databases as well:
1. ProtChemSI (http://pcidb.russelllab.org/) the database of Protein-Chemical Structural Interactions includes all existing 3D structures of complexes of proteins with low molecular weight ligands. When one consideres the proteins and chemical vertices of a graph, all these interactions form a network. Biological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein would bind the other.
Reference: Kalinina OV, Wichmann O, Apic G, Russell RB (2011). Combinations of protein-chemical complex structures reveal new targets for established drugs. PLoS Comp Biol 7(5): e1002043.
2. CLC Drug Discovery Workbench, may freely download from (http://www.clcbio.com/products/clc-drug-discovery-workbench/#download) is new virtual lab bench. On the same webpage you can see its lots of benefits. It gives you access to atomic level insights in protein-ligand interaction, and allows new ideas for improved binders to be quickly tested and visualized.The workbench empowers bench chemists as well as computational chemists to analyze and visualize protein targets and ligands binding to them. The intuitive and powerful interface is designed to communicate with all chemists, with no assumptions about their level of theoretical training. Medicinal chemists can visualize and model molecule interactions to work with ideas in a frictionless manner, thus fueling innovation.
3. Search Tool for Interactions of Chemicals (STITCH) which is Interaction Networks of Chemicals and Proteins and resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.
Reference: http://nar.oxfordjournals.org/content/36/suppl_1/D684.full-text-lowres.pdf
Last time I checked, all those webservices were working for the task:
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Target predictions for any compound in CHEMBL:
https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL25/
https://www.molinspiration.com/cgi-bin/properties
http://moltarpred.marseille.inserm.fr/
http://www.pharmaexpert.ru/
http://ppb2.gdb.tools/
http://rfqsar.kaist.ac.kr/home.php
http://sea.bkslab.org/
http://cheminfo.charite.de/superdrug2/index.html
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Note, you might find some more in there:
http://www.vls3d.com/links/chemoinformatics/off-targets-repurposing
And, look for "target prediction" in the following link:
https://www.click2drug.org/index.html#Homology%20Modeling
Please see following web servers:
ChemProt : http://potentia.cbs.dtu.dk/ChemProt/
SEA: http://sea.bkslab.org/
HitPick: http://mips.helmholtz-muenchen.de/hitpick/cgi-bin/index.cgi?content=targetPrediction.html
SwissTargetPrediction: http://www.swisstargetprediction.ch/
idTarget: http://idtarget.rcas.sinica.edu.tw/
CSNAP: http://services.mbi.ucla.edu/CSNAP/
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