Structure Based Drug Discovery

Bioinformatics Bookmarks

1. PDB Database - RCSB
2. [HPRD]Human Protein Reference Database
3. Ligand-Depot: Search RCBS by ligand (Sketch the ligand)
4. Kyte-Doolittle Hydropathy Plot
5. Welcome to UMBER
6. A Guide to Structure Prediction
7. Bioinformatic tutorials
8. PDBsum - A database of the known 3D structures of proteins and nucleic acids
9. NEW RCSB Protein Data Bank
10. Haystack Project
11. BIND - The Biomolecular Interaction Network
12. PLoS Computational Biology
13. Introduction to QSAR Methodology
14. The Infobiosud PROPSEARCH Server
15. ExPASy - Tools
16. nodalpoint.org | A bioinformatics weblog
17. LionDB
18. The Taverna Project Website
19. BioPAX Home
20. KEGG: Kyoto Encyclopedia of Genes and Genomes
21. The Sequence Manipulation Suite
22. SYSTERS: Large-scale Protein Clustering and Protein Family Database
23. Entrez Utilities
24. EMBL Dali: email server for 3-D protein structure database searches
25. iHOP - Information Hyperlinked over Proteins
26. Wasserman Lab Online Tools
27. UCSC Genome Browser Home
28. Tools
29. ClustalW
30. Biochem 875 | Biochemistry | UW?Madison
31. NCBI BLAST
32. Sketch a Molecule and Search RCBS database
33. Hydropathicity Plots
34. Tutorial in Bioinformatics
35. Homology Modelling
36. Map Viewer

A nice set of Tutorials, notes, reviews about Drug Discovery can be found in the following links:

Practical II: Sequence Retrieval & Alignment

Pracltical II: Homology Modelling

Practical III part1a: Nuclear Receptor Functioning

Practical III part1b: Docking/Screening Tutorial

Practical III part2a: 2D Searching Tutorial

Practical III part2b: 3D Pharmacophore Searching Tutorial

Practical III part2c: ADME Tutorial

Practical III part3: CoMFA Tutorial

Practical IV part1a: Lead Optimization

Practical IV part1b: MD Tutorial

Practical IV part2: QM in Drug Design Tutorial

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Background on the ERα receptor

Visualization of the ERα receptor

Multiple alignment of the ERα Receptor

Multiple alignment of the ERβ receptor

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Lectures

Reviews

Auxiliary Files

Presentations

Link to main Page

Thanks to
Course Director: Prof. Dr. Jacob de Vlieg Course Coordinator: Dr. G. Schaftenaar

Search IUPAC Nomenclature

You know the name of a compound, say methylenedioxy, but do not know the structure of it. One of the easiest online way is to search for compound name in http://www.acdlabs.com/iupac/nomenclature/#search

Search for methylenedioxy resulted in following output:

A cyclic acetal in which the two acetal-oxygen atoms form part of a ring may be named: (a) as a heterocyclic compound; (b) by use of the prefix "methylenedioxy-" for the group as a substituent in the remainder of the molecule, derivatives of the methylenedioxy group being named as substitution products thereof; or (c) particularly when stereochemistry is implied in the name of the corresponding alcohol or ketone, as the alkylene or alkylidene derivative of that alcohol or as the alkylene or alkylidene acetal of that ketone.

A nice notes about Homology modelling

http://ncisgi.ncifcrf.gov/~ravichas/HomMod/

1) PubMed

http://pubmed.gov/
PubMed is a service of the National Library of Medicine that includes over 15 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources.

2) Google Scholar

http://scholar.google.com/
Searches for scholarly literature, including peer-reviewed papers, theses, books, preprints, abstracts and technical reports from all broad areas of research.

3) Scirus

http://www.scirus.com/srsapp/
Scirus is the most comprehensive science-specific search engine on the Internet. Driven by the latest search engine technology, Scirus searches over 200 million science-specific Web pages.

4) HighWire Press

http://highwire.stanford.edu/
HighWire Press is a division of the Stanford University Libraries, which produces the online versions of high-impact, peer-reviewed journals and other scholarly content. Recipient of the 2003 ALPSP Award for "Service to Not-for-Profit Publishing", HighWire partners with influential scholarly societies, university presses and publishers to create a collection of the finest, fully searchable research and clinical literature online. Together, these partners produce nearly half of the 200 most-frequently-cited journals publishing in science.

Interesting compchem links:

• http://www.caddinformatics.com/
• http://www.google.com/Top/Science/Chemistry/Computational/Research_Groups/
• http://www.whatislife.com/

      If the machine is on a network and has only the NFS client operating system software installed (i.e., not the NFS server software as well), a SYBYL session running on that machine will fail to open databases residing on NFS mounted disks connected to a remote machine. When a database is tried to open one wll encounter CANT_GET_LOCK error.

      Installing NFS server operating system software may fixe the problem. This problem does not occur if the machine is completely stand-alone or the NFS server operating system software is installed.

Structure
Based
Drug
Discovery

Interesting links:
http://www.chem.ucsb.edu/~kalju/library/lib_drugs.html
http://www.chemquest.uk.com/AIDS_success.html
http://rmcbiosciences.blogspot.com/