Rosetta Ligand Docking with Flexible XML Protocols

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 819)

Abstract

RosettaLigand is premiere software for predicting how a protein and a small molecule interact. Benchmark studies demonstrate that 70% of the top scoring RosettaLigand predicted interfaces are within 2Å RMSD from the crystal structure [1]. The latest release of Rosetta ligand software includes many new features, such as (1) docking of multiple ligands simultaneously, (2) representing ligands as fragments for greater flexibility, (3) redesign of the interface during docking, and (4) an XML script based interface that gives the user full control of the ligand docking protocol.

Key words

Rosetta RosettaLigand Ligand Docking Small molecule Flexible Flexibility Interface 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of ChemistryVanderbilt UniversityNashvilleUSA

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