Macromolecular Modeling Blog ™

Recent Literature Review

Nir London — Fri, 27 Aug 2010 14:07:58 +0000

A collection of interesting papers from the recent literature - there something for everyone here. Enjoy.

Enhanced paper reading and huge kinase complexes

Nir London — Sat, 14 Aug 2010 20:39:32 +0000

About a year ago we reported of PLoS and Molsoft launching a new way of publishing structural biology related papers. A couple of days ago I've stumbled on one such paper, published in PLoS biology and decided to take the technology for a ride.

2010 Cryo-EM Modeling challenge

Nir London — Thu, 15 Jul 2010 19:52:32 +0000

Cryo-EM single particle analysis is a method for determining structures of large molecules and macromolecular assemblies at resolutions ranging from 3.5-30 A. Interpreting the density maps produced by this technique represents an ongoing challenge, for which molecular modeling techniques offer some unique solutions. In this challange publicly available cryo-EM densities for a selected set of structures at different resolutions, will be provided and challenge those in the modeling community to apply their tools to extract as much information as they can from each.

Jobs Wanted

admin — Wed, 14 Jul 2010 17:59:42 +0000

We launched a new Jobs page. If you're looking to hire - fill in the form at the top of the page. If you're looking for a molecular modeling job - search the jobs (posted in reverse chronological date) We hope this resource would help both employers and modelers.

Postdoctoral fellow – Biotherapeutics @ Pfizer Inc.

Xavier Ambroggio — Mon, 12 Jul 2010 12:54:11 +0000

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 [...]

PDB mode for Emacs

Nir London — Sat, 03 Jul 2010 13:00:45 +0000

Are you tired of mannually editing PDB files ? Checkout this PDB mode for Emacs that helps you do most of the usual modeler editing tasks in a press of a button. Via @leninwtigger

Computational Structural Biology Specialist at Lockheed Martin and NIH

Xavier Ambroggio — Wed, 16 Jun 2010 20:07:35 +0000

JOB DESCRIPTION We are searching for a highly motivated scientist with expertise in macromolecular structure analysis, modeling, and prediction, molecular docking, and/or molecular dynamics simulations to support the National Institute of Allergy and Infectious Diseases (NIAID) within the National Institutes of Health (NIH). This opportunity is a permanent, full-time position with Lockheed Martin MSD and [...]

Jobs in Rosetta Commons Labs

Xavier Ambroggio — Wed, 16 Jun 2010 19:55:53 +0000

There is a new website for job openings in Rosetta Commons labs: http://www.rosettacommons.org/positions/index.html I highly recommend working with any of the PI’s in the Rosetta Commons labs. They’re great folks and great scientists (and most of the labs happen to be in great locations too!). Random Posts

Can we predict small-molecules binding affinities?

Nir London — Fri, 21 May 2010 11:20:03 +0000

In a recent post, Derek Lowe, from "In The Pipeline", asks his readership "If we could just walk right up and calculate the free energies of binding events reliably, what would you most want such calculations to be able to do for you? What would convince you that they're actually believable? And how close to you think that we actually are to that?" We tried tobriefly answer some of these questions. How close are we to predict small molecules binding free energy?

Is dynamics the missing link for understanding enzyme catalysis?

Nir London — Wed, 12 May 2010 18:20:52 +0000

How do enzymes catalyze reactions? There are countless answers of course, but one answer that has gained much attention and popularity in recent years is - through intrinsic dynamics. Is that so? PNAS recently published a paper by Arieh Warshel entitled: "Enzyme millisecond conformational dynamics do not catalyze the chemical step". Warshel, an avid assailant of the coupling between dynamics and catalysis was met by Martin Karplus, devoted advocate for catalytic dynamics, to engage in a public dispute over the letters section of PNAS. Who do you find more convincing?