Doing Simulation using Discovery Studio 2.1

Ashok Kumar — Sat, 20 Feb 2010 23:29:45 +0000

The protocols and tools under Simulation allow you to run energy calculations, solvation, energy minimization, and molecular dynamics simulations using the CHARMm and other programs.

The protocols under Simulation serve the following types of users:

Novice protein modelers and computational chemists who are interested primarily in running pre-defined simulation protocols to provide simple minimization or dynamics of the molecular structure under study. Novice protein modelers and computational chemists will find that the protocols are an easy way to run predetermined workflows with a minimal amount of configuration.
Expert protein modelers and computational chemists who are interested in running several simulation steps independently and trying out different parameterizations.

Analysis Goals

You can use Simulation methods to:

Analyze molecular trajectories
Calculate energies using molecular mechanics or QM-MM based methods
Calculate interaction energies
Equilibrate a molecule with molecular dynamics
Perform a dynamics simulation to adjust the temperature of a molecule
Perform molecular dynamics on a pre-equilibrated molecule
Minimize a molecule using molecular mechanics or QM-MM
Calculate the radial distribution function for two sets of atoms in a trajectory
Solvate a system by adding water molecules
Perform a set of minimization and equilibration steps followed by molecular dynamics
Calculate fundamental motions (Principal Components) of a trajectory
Prepare structures for simulation using the forcefield tools
Apply constraints on atoms in structures before performing simulation analysis
Analyze molecular trajectories

Simulation Tasks

The following table describes the basic tasks that are possible with the Simulation methods. Read more..

Protein Modeling using Discovery Studio 2.1

Ashok Kumar — Mon, 18 Jan 2010 15:53:19 +0000

Experimental structure determination involves difficult methods that require a significant amount of expertise and resources. Protein Modeling on the other hand enables access to sensible structural models in much shorter periods of time. The major aim of protein modeling is the prediction of a protein’s tertiary structure from its primary structure. To this end a diverse range of approaches have been developed comparative, de novo or ab initio structure prediction.

The protein modeling methods provided in Discovery Studio provide an extensive set of tools for the construction of molecular structures and analysis of their behavior.

Protein Modeling in Accelrys Discovery Studio 2.1

Analysis Goals

Protein Modeling provides tools and protocols that allow you to:

Build and edit proteins or peptides
Modify protein structures and generate reports of protein structures
Identify and report abnormalities in a protein structure
Align sequences according to sequence similarity or structure similarity
Build homology models for a protein sequence
Refine side-chain conformation of a protein structure
Refine conformation of one or more loop regions of a protein structure
Mutate residues and optimize structure
Predict protein docking conformations
Model antibody structure and variable loop conformations
Analyze the sequence conservation pattern of a sequence family
Identify conserved functional patches in a protein structure

Protein Modeling Tasks

The following table describes the basic tasks that are possible with the Protein Modeling methods in Discovery Studio. Click here for tutorial….

BioGem.Org » Accelrys

Doing Simulation using Discovery Studio 2.1

Protein Modeling using Discovery Studio 2.1