Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Warren L Delano Memorial Fund
From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2009-11-15

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Subject: Re: video that explains, very simply, what Structural Molecular Biology is about
From: Konrad Hinsen hinsen {- at -} CNRS-ORLEANS {- dot -} FR
Date: 2009-11-16

Subject: Re: video that explains, very simply, what Structural Molecular Biology is about
From: Christoph Best best {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2009-11-15

Hello everybody-

> Molecular models are the result of numbers emerging from computer programs.
> The results of such computations do not reflect anything in nature. There's
> no experimental evidence whatsoever, making modelling a very theoretical --
> in my eyes uninteresting -- exercise.

Molecular dynamics is starting to incorporate experimental evidence into
molecular dynamics simulations, e.g. from EM

Flexible Fitting of Atomic Structures into Electron Microscopy Maps
Using Molecular Dynamics

Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank,
Klaus Schulten

Structure. 2008 May; 16(5): 673â€“683.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430731/?tool=pubmed

(This stills needs an X-ray structure as starting point). We are already
frequently confronted in EM with deciding how much of a fitted structure
is modeling and how much is supported by evidence. At some point it is a
matter of degree, not principle. (This point is where you can see mostly
blobs).

By the way, molecular dynamics, which is based on first principles, is
quite different from (homology) modeling in bioinformatics. The latter
is indeed merely a very educated guess that often works.

Oh, and the last paragraph of the paper is interesting...

-Christoph

--

Dr Christoph Best http://www.ebi.ac.uk/~best

Project Leader Electron Microscopy Data Bank, PDB Europe

European Bioinformatics Institute, Cambridge, UK +44-1223-492649

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Warren L Delano Memorial Fund
From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2009-11-15

Next message:
Subject: Re: video that explains, very simply, what Structural Molecular Biology is about
From: Konrad Hinsen hinsen {- at -} CNRS-ORLEANS {- dot -} FR
Date: 2009-11-16