Category: Databases

Current Protocols from Wiley @WileyScience

2/26/2013

Current Protocols from the Wiley online library offer protocols in several areas such as Bioinformatics, Cell Cultures, Chemical Biology, Molecular Biology, Pharmacology and Drug Discovery and many more. They are not free, but most academic libraries should have a subscription.

Here is the list for protocols on Molecular Modeling:

Protein Structural Domains: Definition and Prediction
Iakes Ezkurdia, Michael L. Tress
Published online: November 2011
Using AutoDock for Ligand‐Receptor Docking
Garrett M. Morris, Ruth Huey, Arthur J. Olson
Published online: December 2008
Exploring Biological Networks with Cytoscape Software
Natalie Yeung, Melissa S. Cline, Allan Kuchinsky, Michael E. Smoot, Gary D. Bader
Published online: September 2008
Browsing Multidimensional Molecular Networks with the Generic Network Browser (N‐Browse)
Huey‐Ling Kao, Kristin C. Gunsalus
Published online: September 2008
Using ChemBank to Probe Chemical Biology
Kathleen Petri Seiler, Heidi Kuehn, Mary Pat Happ, Dave DeCaprio, Paul A. Clemons
Published online: June 2008
Comparative Protein Structure Modeling Using MODELLER
Narayanan Eswar, Ben Webb, Marc A. Marti‐Renom, M.S. Madhusudhan, David Eramian, Min‐yi Shen, Ursula Pieper, Andrej Sali
Published online: November 2007
In Silico Drug Exploration and Discovery Using DrugBank
David S. Wishart
Published online: June 2007
Minimotif Miner: A Computational Tool to Investigate Protein Function, Disease, and Genetic Diversity
Martin R. Schiller
Published online: May 2007
Comparative Protein Structure Modeling Using Modeller
Narayanan Eswar, Ben Webb, Marc A. Marti‐Renom, M.S. Madhusudhan, David Eramian, Min‐yi Shen, Ursula Pieper, Andrej Sali
Published online: October 2006
Using MSDchem to Search the PDB Ligand Dictionary
Dimitris Dimitropoulos, John Ionides, Kim Henrick
Published online: October 2006
Representing Structural Information with RasMol
David S. Goodsell
Published online: October 2005
Protein Tertiary Structure Prediction
Dong Xu, Ying Xu
Published online: May 2001
Protein Tertiary Structure Modeling
Nicolas Guex, Torsten Schwede, Manuel C. Peitsch
Published online: May 2001

Zoe

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Databases for Chemical Structure Search

1/14/2013

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Apart from the well-known SciFinder database, free databases for chemical structure search are the following:

1) Pubchem. PubChem, released in 2004, provides information on the biological activities of small molecules. PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links in the homepage.
Links from PubChem's chemical structure records to other Entrez databases provide information on biological properties.

2) ChemSpider. ChemSpider is a free chemical structure database providing fast text and structure search access to over 28 million structures from hundreds of data sources.

3) ChemFrog. ChemFrog is a chemical database that offers over 1 million commercially available chemicals and vendor information.

4) ChemDB. ChemDB is the IGB Chemical Database: The most diverse and useful set of chemoinformatics tools and applications available to the public. Applications: Chemical Search Find a chemical by basic criteria like molecular weight and predicted logP, or by the more abstract notion of structural similarity. Virtual Chemical Space Interactively deconstruct target compounds into component precursors and reconstruct similar building-blocks into combinatorial libraries representing the "virtual chemical space" near the target compound. Reaction Explorer Interactive system for learning and practicing reactions, syntheses and mechanisms in organic chemistry, with advanced support for the automatic generation of random problems, curved-arrow mechanism diagrams, and inquiry-based learning. COSMOS Predicts 3D small molecule structures from various standard 2D formats Reaction Predictor Predicts Mechanistic Reactions Using Machine Learning.

5) iScienceSearch. An Internet search engine for chemists. iScienceSearch also supports mobile devices and it works well to draw structures on something like an iPad. We use JSDraw from Scilligence (www.scilligence.com) to draw chemical structures. This is a good application to find out for yourself if mobile devices are useful for research. Please remember to allow pop-ups otherwise you don’t see the result page. Links to tools that predict biological activities and many other parameters of a structure, like logP are incorporated. PASS (Prediction of Activity Spectra of Substances) (www.akosgmbh.de/pass) predicts with high accuracy about 4000 effects for a compound.

6) Chemicalize (www.chemicalize.org ) from ChemAxon calculates structure parameters.

7) The DistilBio (a powerful, federated, life sciences search engine) new release now has instant display of results. http://distilbio.com With instantaneous search results and auto-complete, it is now even easier to find the research you are looking for all in one place. Visit the site and try it with "Aspirin".

Zoe

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Current Protocols from Wiley @WileyScience

Databases for Chemical Structure Search

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