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
Analysis of Protein Binding Sites by Computational Solvent Mapping
Evolutionary Trace for Prediction and Redesign of Protein Functional Sites
Information Entropic Functions for Molecular Descriptor Profiling
Virtual Screening of Large Compound Libraries: Including Molecular Flexibility
Expanding the Conformational Selection Paradigm in Protein-Ligand Docking
Flexibility Analysis of Biomacromolecules with Application to Computer-Aided Drug Design
On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening
Virtual Ligand Screening Against Comparative Protein Structure Models
AMMOS Software: Method and Application
Rosetta Ligand Docking with Flexible XML Protocols
Normal Mode-Based Approaches in Receptor Ensemble Docking
Application of Conformational Clustering in Protein–Ligand Docking
How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries
Prediction of Protein-Protein Docking and Interactions
AGGRESCAN: Method, Application, and Perspectives for Drug Design
ATTRACT and PTOOLS: Open Source Programs for Protein–Protein Docking
Prediction of Interacting Protein Residues Using Sequence and Structure Data
Rescoring Docking Predictions
MM-GB/SA Rescoring of Docking Poses
A Case Study of Scoring and Rescoring in Peptide Docking
The Solvated Interaction Energy Method for Scoring Binding Affinities
Linear Interaction Energy: Method and Applications in Drug Design
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
Analysis of Protein Binding Sites by Computational Solvent Mapping
Evolutionary Trace for Prediction and Redesign of Protein Functional Sites
Information Entropic Functions for Molecular Descriptor Profiling
Virtual Screening of Large Compound Libraries: Including Molecular Flexibility
Expanding the Conformational Selection Paradigm in Protein-Ligand Docking
Flexibility Analysis of Biomacromolecules with Application to Computer-Aided Drug Design
On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening
Virtual Ligand Screening Against Comparative Protein Structure Models
AMMOS Software: Method and Application
Rosetta Ligand Docking with Flexible XML Protocols
Normal Mode-Based Approaches in Receptor Ensemble Docking
Application of Conformational Clustering in Protein–Ligand Docking
How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries
Prediction of Protein-Protein Docking and Interactions
AGGRESCAN: Method, Application, and Perspectives for Drug Design
ATTRACT and PTOOLS: Open Source Programs for Protein–Protein Docking
Prediction of Interacting Protein Residues Using Sequence and Structure Data
Rescoring Docking Predictions
MM-GB/SA Rescoring of Docking Poses
A Case Study of Scoring and Rescoring in Peptide Docking
The Solvated Interaction Energy Method for Scoring Binding Affinities
Linear Interaction Energy: Method and Applications in Drug Design
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