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Computational Drug Discovery and Design volume from @SpringerPub

3/1/2013

0 Comments

 
Riccardo Baron also put together a great computational methods volume you should have access to:http://link.springer.com/book/10.1007/978-1-61779-465-0/page/1
Here's the list of contents:

Drug Binding Site Prediction, Design, and Descriptors
A Molecular Dynamics Ensemble-Based Approach for the Mapping of Druggable Binding Sites
  • Anthony Ivetac, J. Andrew McCammon Look Inside Get Access
Analysis of Protein Binding Sites by Computational Solvent Mapping
  • David R. Hall, Dima Kozakov, Sandor Vajda
Evolutionary Trace for Prediction and Redesign of Protein Functional Sites
  • Angela Wilkins,Serkan Erdin,Rhonald Lua,Olivier Lichtarge
Information Entropic Functions for Molecular Descriptor Profiling
  • Anne Mai Wassermann,Britta Nisius,Martin Vogt,Jürgen Bajorath

Virtual Screening of Large Compound Libraries: Including Molecular Flexibility
Expanding the Conformational Selection Paradigm in Protein-Ligand Docking
  • Guray Kuzu,Ozlem Keskin,Attila Gursoy,Ruth Nussinov Look Inside Get Access
Flexibility Analysis of Biomacromolecules with Application to Computer-Aided Drug Design
  • Simone Fulle,Holger Gohlke
On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening
  • Sara E. Nichols,Riccardo Baron,J. Andrew McCammon
Virtual Ligand Screening Against Comparative Protein Structure Models
  • Hao Fan,John J. Irwin,Andrej Sali
AMMOS Software: Method and Application
  • T. Pencheva,D. Lagorce,I. Pajeva,B. O. Villoutreix,M. A. Miteva
Rosetta Ligand Docking with Flexible XML Protocols
  • Gordon Lemmon,Jens Meiler
Normal Mode-Based Approaches in Receptor Ensemble Docking
  • Claudio N. Cavasotto
Application of Conformational Clustering in Protein–Ligand Docking
  • Giovanni Bottegoni,Walter Rocchia,Andrea Cavalli
How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries
  • Andrew J. Christofferson,Niu Huang

Prediction of Protein-Protein Docking and Interactions

AGGRESCAN: Method, Application, and Perspectives for Drug Design
  • Natalia S. de Groot,Virginia Castillo,Ricardo Graña-Montes,Salvador Ventura
ATTRACT and PTOOLS: Open Source Programs for Protein–Protein Docking
  • Sebastian Schneider,Adrien Saladin,Sébastien Fiorucci,Chantal Prévost
Prediction of Interacting Protein Residues Using Sequence and Structure Data
  • Vedran Franke,Mile Šikić,Kristian Vlahoviček

Rescoring Docking Predictions
MM-GB/SA Rescoring of Docking Poses
  • Cristiano R. W. Guimarães
A Case Study of Scoring and Rescoring in Peptide Docking
  • Zunnan Huang, Chung F. Wong
The Solvated Interaction Energy Method for Scoring Binding Affinities
  • Traian Sulea, Enrico O. Purisima
Linear Interaction Energy: Method and Applications in Drug Design
  • Hugo Gutiérrez-de-Terán, Johan Åqvist 
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Keeping up with the current literature using Google Reader

4/6/2012

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All lab group members should keep up to date with current literature in our field such as
  • J Chem Theory Comput
  • JACS
  • J Phys Chem B
  • J Med Chem
  • Angewandte Chemie IE
Google Reader offers an easy way to read titles + graphical abstracts of all the publications in one go. Follow these steps:
  1. Get a google account
  2. Login into Google Reader
  3. Go to your favorite journal's page and look for a link called "RSS FEED". Copy that link location.
  4. In Google Reader click on "Subscribe" and paste the link you copied above.
  5. Now you are subscribe to that journal's updates: If you do not click on an article as you scroll down the titles, the title will disappear. You can mark an abstract as "unread" if you want to keep it in your list.
  6. You can also link to other interesting webpages, ie our lab's blog RSS feed link is: http://www.drugdesign.gr/1/feed
So here is how Google Reader should look like:
Picture
Below is a 1-min video on how to use Google Reader. Enjoy reading!

Zoe

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    Alexis, Maria, Dimitra, Ioannis,  Michalis, Danai, Panos, George, Aspa, Zoe

    lab group members!

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