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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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Current Protocols from Wiley @WileyScience

2/26/2013

0 Comments

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

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