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Structure Based Drug Discovery

SBDD: Recipes, Ideas and Links...

Cool Bioinformatics Pointers

Wednesday, October 19, 2005
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
  32. Sketch a Molecule and Search RCBS database
  33. Hydropathicity Plots
  34. Tutorial in Bioinformatics
  35. Homology Modelling
  36. Map Viewer

Pointers to "Computational Drug Discovery Course"

Tuesday, September 20, 2005
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

Background on the ERα receptor
Visualization of the ERα receptor
Multiple alignment of the ERα Receptor
Multiple alignment of the ERβ receptor

Auxiliary Files
Link to main Page

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

Structure search by name (IUPAC Nomenclature search)

Thursday, September 15, 2005

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.

Homology Modeling: Concepts and Protocols

Tuesday, September 13, 2005
A nice notes about Homology modelling


Scientific Search Engines

Thursday, August 18, 2005
1) PubMed

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

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

3) Scirus

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

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.

bioinformatics links

Tuesday, August 16, 2005
Interesting compchem links:

Sybyl, CANT_GET_LOCK error MDB

      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.


Friday, August 12, 2005

Interesting links: