Macromolecular Modeling Blog ™

A postdoctoral researcher is sought to conduct fundamental computational research to understand molecular origins of aggregation in protein therapeutics, especially monoclonal antibodies and antibody based therapeutics. The research shall involve an inter-disciplinary mix of statistical analyses, bioinformatics, high performance grid computing, molecular biophysics, molecular modeling, and simulation techniques to advance our understanding of protein structure-function-aggregation relationships and mechanism(s) of aggregation. The researcher shall be expected to develop novel approaches to detect aggregation prone regions and three dimensional aggregation prone motifs and suggest ways to improve manufacturability of biotherapeutics via rational design.

For detailed job focus, responsibilities and qualifications, please access http://www.pfizer.com/careers and use code 941315.

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Rosetta 3.0 was release on the Rosetta Commons website last Friday, February 27th.  Rosetta 3.0 is a whole new Rosetta developed in a purely object oriented manner.  Most functionality from previous versions of Rosetta have been ported over and tested, ensuring very similar results.  Rosetta 3.0 is available for download as a BETA version and any users are encouraged to give feedback.

A big improvement over previous versions of Rosetta is the ability to create custom “apps”, as well as compile existing and documented apps as separate executables.  Gone are the days of a single executable all modes with a paragraph worth of flags.  Now, each app has its own executable and flags.

Existing apps that can be compiled and run with no modifications include:

RosettaAbinitio – Performs de novo protein structure prediction.

RosettaDesign – Dentifies low free energy sequences for target protein backbones.

RosettaDesign pymol plugin – A user-friendly interface for submitting Protein Design simulations using RosettaDesign.

RosettaDock – Predicts the structure of a protein-protein complex from the individual structures of the monomer components.

RosettaAntibody – Predicts antibody Fv region structures and performs antibody-antigen docking.

RosettaFragments – Generates fragment libraries for use by Rosetta ab initio in building protein structures.

RosettaNMR – Incorporates NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction.

RosettaDNA – For the design of proteins that interact with specified DNA sequences.

RosettaRNA – Fragment assembly of RNA.

RosettaLigand – For small molecule – protein docking.

These are days of a world wide economic turmoil, most of the industry is effected and the academia as well. But even within the academia, certain fields are funded better than others. What happened to the molecular modeling funding?

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