May
08
2014
0

Webinar: AMBER 14 & GPUs – Creating the World’s Fastest MD Package

Please join us on May 13th for a webinar presented by Professor Ross Walker of UC San Diego, Professor Adrian Roitberg of University of Florida and Scott Le Grand of Amazon Web Services. This webinar will provide an overview of the AMBER Molecular Dynamics Software package with focus on new GPU accelerated features in the recently released version 14. This includes details of peer-to-peer support and optimizations, which have resulted in version 14 being the fastest MD software package on NVIDIA GPUs. Other GPU features include support for multi-dimensional replica exchange MD, hydrogen mass repartitioning, and support-as-a-service on Amazon Web Services. Benchmarks will be provided, along with recommended hardware choices. This webinar is planned for May 13th 2014 at 9.00 AM Pacific Time. Register at: http://bit.ly/AMBER14

by guest author: Perri Needham, UCSD

Nov
02
2013
0

Molecular Dynamics, believe it or not

Anthony Nicholls (of OpenEye scientific software, Cambridge, MA) recently gave a critical talk on the usage and reporting of Molecular Dynamics simulations. Luckily Ash from The Curious Wavefunction was there to beautifully summarize the main points. I urge you to head over and read the full summary. Below are the main headlines.

  • MD is not a useless technique but it’s not held up to the same standards as other techniques, and therefore its true utility is at best unknown
  • MD can accomplish in days what other techniques can achieve in seconds or hours
  • MD can look and feel “real” and seductive
  • Using jargon, movies and the illusion of reality, MD oversells itself to the public and to journals
Written by admin in: Weird science | Tags: ,
May
06
2011
3

Annotatr and The MD Club

Some months ago, Bosco Ho, Molecular Dynamics (MD) boy wonder and HTML5 wiz, contacted a group of scientists, myself included, to start a world wide Journal Club (JC). The subject: Molecular Dynamics, the venue? Annotatr – a mashup of CiteULike and Disqus. The motivation behind Annotatr was to get scientists to comment on articles (lower the energy barrier if you prefer).

Since then the MD JC had several prolific sessions, discussing some great MD papers on which I’ll discuss briefly below, as well as recently, a completely unrelated theoretical evolutionary paper just to broaden our horizons.

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May
24
2009
0

Molecular Dynamics Vs. Monte Carlo

I’m happy to cross-post another elegant piece written by the MD specialist Bosco Ho. In this post Bosco compares the performance of Molecular Dynamics simulations with Monte Carlo simulations in reconstructing NMR S order parameters for microsecond biological processes. Curious to know which is better ?

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Dec
18
2008
0

Model for the Peptide-Free Conformation of Class II MHC Proteins

Although numerous structures of peptide bound MHC-II molecules were solved, no one knows how does the peptide free MHC look like. Painter et al. elegantly use molecular dynamics to model the conformational changes upon peptide removal. Most interestingly a helix from the peptide binding domain adopts the binding mode of the antigen peptide. They successfully validate their model using antibodies and superantigens, predicted to differentially bind peptide-bound/free molecules according to their model. We take the validation one step further and propose mutations based on Painter’s model that would stabilize the free MHC. Will it work? Who will pick up the gauntlet?

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Dec
11
2008
0

Structural and Thermodynamic Approach to Peptide Immunogenicity

Carlos J. Camacho et al. study the relationship between peptide stabilities and their immunogenicity. They present a model system of several peptides corresponding to portions of murine HRS which are capable of inducing anti-protein antibodies of varying affinity and temporal persistence. On this system they show by molecular dynamics simulations, that sequences of the most immunogenic peptides correspond to highly ordered structural motifs in the parent protein. Competitive ELISAs provide direct evidence that these peptides share structural determinants with native protein. More interestingly they address the question of how can these less stable peptides induce the same immunogenic response. By Nir London

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Nov
14
2008
0

Stability and structural recovery of the tetramerization domain of p53-R337H mutant induced by a designed templating ligand

S. Gordo et al. implement a new strategy for preventative anti-cancer therapeutics. R337H is the most frequent inherited mutation in p53, “The guardian of the genome”, and is associated with wide spectrum of cancer forms. The mutation is believed to destabilize the native tetramer form of p53. In this study the researchers designed a small molecule that reconstitutes tetramerization of such a mutant. By Nir London.

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Oct
31
2008
3

Incorporating Flexibility Into Docking Using Normal Mode Analysis

Incorporation of flexibility into docking simulations and accounting for backbone conformational changes during association is probably the toughest problem protein-protein dockers are facing today. Normal Mode Analysis is lately the answer of many groups to this problem. We hereby review two approaches of incorporating NMA into docking simulations, reflecting the induced fit vs. conformational sampling association mechanisms. 

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