HELP! Protein Graphics!! Sorry, No help available on that topic

Barani barani at mace.cc.purdue.edu
Sun Jan 29 13:22:42 EST 1995



>Article: 3561 of bionet.molbio.proteins

>Lluis from Massachvsettes Institvte of Technology writes:-
>
>This is a lot of baloney !!, typical crystallographer's self-protecting
>speech. The fact of the matter is that if your protein Y is a totally 
>new enzyme you can dramatically speed up your biochemical 
>characterization if you can model its structure.
> Molecular modeling is a low resolution technique by comparision to
>experimental methods, that is implicit in the system. However it can
>provide information several orders of magnitude faster than crystallography.
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  Small Correction here:- I guess the sentence should probably read as
 
 "provide WRONG information several orders of magnitude faster than
  crystallography"
 
  :-)
 
> To say that a model should provide a good solution to a molecular
> replacement search is also nonsense. That is not what should be 
>expected from a model.
>
  uh Oh.. that is not what my teacher taught me..hmm..why do they waste
  thousands of pages publishing self and cross rotation functions..
  
>
> Once again you confuse the subject, Nature has surprises even for the most
>studied of structures (i.e. haemoglobin) what counts is the level of certanty
>that you expect to obtain from your analysis. The whole bunch of methods that
>we use today for protein modeling (from sequence alignments to structure 
>analysis
>by statistical force fields) provide us with good tools to get a good initial
>approximation to a problem. 
>No modeller will never refuse to use x-ray data, and no crystallographer 
>should
>ignore the information that modeling techniques can provide. The RAS structure
>would have been proved wrong by several modeling statistical methods had 
>they been used to analyze it. 
>Don't you think that part of the crystallographer's despise for modeling stems
>from they anger at loosing the monopoly of structure determination ?.

 Let me remind you a familiar Story:-

 What do 5 protein modellers make by combining

 (1) 4 pillars (2) a cylinder (3) a snake (4) two handfans (5) a barrel?

     An ELEPHANT !!!

 On the serious side:- 

 For your kind information we crystallographers do not despise anyone
 and we too use modelling techniques and tools as essential parts of
 our work. IMHO crystallographers are more closer to the truths 
 of a biomolecule than anyone else.  From my small experience I can 
 say that a distance of 0.2 A between two non bonded atoms out of 
 13,000 atoms makes the difference between whether I have solved 
 the structure or not. I doubt if modellers have scratched their 
 head and spent two months about such a small measure that stands
 between truth and a model-protein which won't convert glucose into
 glycogen.

 Let us go back to the real topic:- HELP! Protein Graphics!!

 As of today there is no successful program or algorithm that can
 model a protein based on sequence and there are a few thousand
 scientists who would lose their jobs if there is one! And for their
 sake let there not be one !!

 Barani
 B146 Lilly Hall of Life Sciences
 Purdue University

 ps: it would be nice to see your full email address in order to
     take your mail seriously. 
     



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