Bioinformatics

Monday, April 20, 2015

SSH: Connection refused

Was trying to start a X11 from a remote machine and got "Connection refused" error message. Checked few forums, but couldn't find a solution.

Absolutely my mistake :(

Used -x instead of -X when I logged in from my PC to cluster head, and from cluster head to qsub interactive session I used 'qsub -I -X'.

The solution is: just a login with -X :)

Friday, May 25, 2007

Computational chemistry and Drug designing

Drug Design

Links on Drug Design, compilation of answers to a CCL question posed in February 2000.

There is a good discussion of the generation and use of large 3D databases in drug discovery which is accessible on-line, from the September 1995 issue of NetSci. It covers pharmacophore-based 3D searches as well as searching in the context of the binding site of a given structural target.

Thomas Wieland's summary of connections between topological indices, similarity, screening and drug design.

Drug Discovery Online - “the first internet site devoted exclusively to drug discovery and early-stage drug development”.

Methods for Structure Based Design - a review article describing docking methods.

NCI Drug Information System 3D Database - a collection of 3D (built) structures of over 400,000 drugs.

The AIDS 3D Database - a database of compounds active in the NCI AIDS Antiviral Screen.

HIV Protease Database (HIVsdb) - 3D structures of HIV-PR inhibited complexes.

World Wide Drugs - many links.

Binding Database - data on noncovalent association, vital for the elucidation of the physical chemistry of molecular recognition and the discovery of new drugs .

HIV Drug Design

Search NIH for “HIV protease” - perform a search of the NIH for documents matching HIV protease.

Computational Chemistry

CCL - the Computational Chemistry List, provides software, an archive of list postings, data, documents, announcements about conferences and jobs, as well as links to other web sites.
SDSC Computational Chemistry - combined program of computational prediction and experimental verification, to understand the design principles of molecular construction.
SDSC Chemistry Software - for calculating chemical reactions, molecular modeling, and chemistry visualization.
Journal of Computational Chemistry's Internet Resources - a very good collection of useful sites.
Research Tools from Frontiers in Bioscience.
Encyclopaedia of Computational Chemistry from Wiley.
The Virtual Library:

Network Science (NetSci) - a forum to explore and discuss current applications of science and technology. (Even though its mission sounds general, its focus seems highly molecular and biophysical). June and July's issues are on a fascinating topic: “Assessing Molecular Diversity”; there are articles on combinatorial chemistry, molecular diversity and mass screening. In the April,1996 issue Michael Connolly (“Molecular Surfaces: A Review”) and TJ O'Donnell (“Scientific and Artistic Uses of Molecular Surfaces”) looked at the evolution and use of molecular surfaces.
Scientific Software Lists from Network Science.
Netscape's helper applications page.
In an attempt to bring standards to assist in the exchange of chemical information across the web, a number of types of data have been proposed. Here are the details on the various chemical MIME types.

Proteins, Nucleic Acids and Small molecules

Proteins and Nucleic Acids

The New PDB: Research Collaboratory for Structural Bioinformatics (RCSB)

Protein Data Bank, or “PDB”, hosted at the RCSB. Answers to FAQ.

PDB SearchLite - start your search for proteins here.

PDB SearchFields - advanced search of the protein database.

Protein and Nucleic Acid Databases.

Archive of Obsolete PDB Structures.

Protein Structural Homology.

Protein Families

Family Pairwise Search (FPS) - search a library of protein families with a protein sequence, GCG profile or BLAST checkpoint file that you provide.

Protein Kinase Resource (PKR).

The HET Group Dictionary. Lists the connectivity records of HET groups.

Formats:

PDB Format - a description of the atomic coordinate entry format.

mmCIF: macromolecular Crystallographic Information File, and software tools.

À La Mode - A Ligand and Monomer Object Data Environment.

NDB: The Nucleic Acid Database - structural information about nucleic acids, and its Structure Finder.

Proteins Plus from the NDB.

Quick Search.

Full Search.

PDBSELECT provides a representative list of high-resolution structures.

PDBFINDER is a database that is constructed using a PERL script from the PDB, DSSP and HSSP databases. Many of the fields contained in the PDBFINDER database are difficult to access from the original databases. Some information is retrieved from the original literature.

OBSTRUCT - A service to obtain a largest non-redundant set of protein structures from PDB according to crystallographic resolution and sequence identity as specified by the user. Also NMR-elicited structures can be selected.

PROCHECK - Checks the stereochemical quality of a known protein structure, producing a number of graphical plots analysing its overall and residue-by-residue geometry.

Dali Domain Dictionary.

SCOP - Structural Classification of Proteins in UK and USA.

CATH - Protein Structure Classification.

FSSP: Fold classification based on Structure-Structure alignment of Proteins

HIV Protease Database originally from Alexander Wlodawer's Macromolecular Structure Laboratory at NCI-Frederick Cancer Research and Development Center.

Atlas of Protein Side-Chain Interactions - based on the printed atlas of Singh & Thornton (1992)

The Backbone Dependent Rotamer Library WebPage and the Protein Sidechain Webpage from Roland L. Dunbrack's group.

Molecules R US - from the NIH.

NCBI (National Center for Biotechnology Information) Structure Group.

MMDB: The Molecular Modeling Database - this is a compilation of all the Brookhaven Protein DataBank 3-dimensional structures of biomolecules from crystallographic and NMR studies. (MMDB is a database of ASN.1 -formatted records, not PDB formatted records.)

Structures in MMDB have been compared with one another using VAST (Vector Alignment Search Tool).

Entrez (DNA/RNA + Protein + Structures + Medline subset).

The WWW Virtual Library: Biomolecules.

RNA Secondary Structures.

Image Library of Biological Macromolecules.

Swiss-3DIMAGE -- protein structure images (many stereo)

Antibody Resource Page - compilation of antibody sites and resources for locating antibodies.

Protein Structure Prediction Center - hosts the CASP web sites.

Molecular Information Agent (MIA) - a web server that searches biological databases to find the existing information about a macromolecule.

Small Molecules & Ligands

ReLiBase- “a database system for analysing receptor/ligand complexes deposited in the Protein Data Bank”. Search for complexes that contain a specific substructure, either by sketching a molecule or by typing a SMILES string. Alternatively, seach for a specific interaction, or in other ways.

2D and 3D Structural Information from the DTP (Developmental Therapeutics Program) at the National Cancer Institute 3D Database (NCI DIS 3D database. DIS = Drug Information System) contains some 400,000 drugs. Structures for some 200,000 compounds can be downloaded.

NCI Data and Online Services where you can search the NCI Database of compounds, convert file formats, and find public chemical data .

127,000 NCI open database compounds built by Corina (35MB file compressed, 200MB uncompressed).

140,000 plated compounds (75 MB file compressed, in MDL SD format).

1,980 diversity set compounds (in MDL SD format) representing the chemical diversity of the plated compounds.

Milne, G.W.A., Nicklaus, M.C., Driscoll, J.S., Wang, S. and Zaharevitz. D. ''The NCI Drug Information System 3D Database.'' J. Chem. Inf. Comput. Sci. 34:1219-1224 (1994).

ZINC - a free dockable database project for virtual screening sponsored by the Shoichet Laboratory, Pharmaceutical Chemistry, UCSF, and hosted by docking.org.

KEGG DRUG - a database of drugs approved in the USA and Japan, part of a bioinformatics resource named KEGG (Kyoto Encyclopedia of Genes and Genomes), produced by the Kanehisa Laboratories in the Bioinformatics Center of Kyoto University and the Human Genome Center of the University of Tokyo.

ChemBank - a freely available collection of data about small molecules , from the Institute For Chemistry and Cell Biology, part of Harvard Medical School.

The Three-Dimensional Drug Structure Databank - an NIH collection of experimental and approved therapeutic agents whose structures have been experimentally determined or built. There are not many structures right now (20 structures in March 1996).

CCDC: Cambridge Crystallographic Data Centre and the Cambridge Structural

Database, CSD, of organic and metal organic compounds.

SMILECAS database from Syracuse Research contains more than 103 000 SMILES-Codes and CAS-numbers.

CACTVS Online SMILES Translator and Structure File Generator, really useful if you want to convert from a SMILES string into a 3D structure; it works even with many molecules. Check out all the other goodies from the Erlangen/Bethesda Data and Online Services.

source : http://mgl.scripps.edu/people/gmm/
thanks to sam alidrin (advanced diploma in bioinfo MKU) for sending me this link

Bioinfo Tutorial n e Books

TUTORIALS

NCBI Education click here

Programming Tutorials

Visual Basic tutorial click here

Link for all languages click here

Learn Perl in 21 days click here

Web based practicals

Protein sequence and structure analysis: A practical guide click here

Protein sequence analysis : A Practical guide click here

Bioinformatics and molecular modeling click here

Introduction to Biocomputing click here

Phylogetic analysis demo click here

Using Computers in Molecular Biology click here

Bioinformatics : Genes, Proteins and Computers click here

C40 WWW Practicals click here

Bioinformatics : Elementry Sequnce analysis click here

EMBnet : Biocomputing tutorial click here

Bioinfo tutorials click here

VMD documentation click here

Ebooks

Connotea (Free online reference management for clinicians and scientist) click here

esnips (Upload ur 5 GB of files to share with friends) click here

(need more biology e-books contact me)

Pymol Movies

Pymol Movies

A picture speaks thousand words, so 1000 pictures combined into a 25 seconds movie will speak 1000x1000 words.

There are excellent resources available online to make movies by combining images from Pymol.
One can start from the below link.

http://www.pymolwiki.org/index.php/Making_Movies

I have used several of these resources to create movies for lab presentation. We have also published a movie as supplementary material for an article published in Journal of Physiology.