CCL: Summary on Modelling of DNA-Protein interaction

[Alessandro <a.pandini $#at#$ csrsrc.mi.cnr.it>]

Here is a first Summary... hope to get more later.
 If anyone has something else to add, I will re-post a new Summary later.
 Meanwhile,
 thanks a lot to all who answered.
 Ale
 *****Original Question:*****
 Dear cclers,
 I am looking for some good reviews about DNA-Protein interaction, both
 on modelling and calculations.
 Despite some experiences on protein studies, I have no idea on DNA
 problems... so pratical suggestion on this topics are gratefully
 accepted, too.
 This is a "first look"  search, just for getting an idea of the state
 of
 the art, so every good information could be useful.
 Thanks a lot.
 Ale
 *****Summary*****
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 From: Tanja van Mourik
 The following two papers contain some information on DNA-protein
 complexes:
 "Hydration of DNA: take 2", H.M. Berman, Current Opin. Struct. Biol.
 4,
 345-350 (1994)
 "Weakly Bound Clusters of Biological Interest", C. Desfrancois, S.
 Carles
 and P.J. Schermann, Chem. Rev. 100, 3943-3962 (2000) (paragraph 4.3)
 -----
 From: Dr Mark J Forster Ph.D.
 Several programs are available for docking two macromolecules when
 one of them (typically the protein) is held rigid and then replaced by a
 grid. The Sterberg group have a code (Multidock) which allows
 full flexibility, see their web page
 http://www.bmm.icnet.uk/multidock/multidock.html
 The Nussinov group (ref 4) are also publishing reports on flexible
 docking but I am not sure if their codes are available. Their work
 focusses on protein-protein complexes.
 (1) Predictive docking of protein-protein and protein-DNA complexes.
 Sternberg MJ, Gabb HA, Jackson RM
 Curr Opin Struct Biol. 1998 Apr;8(2):250-6. Review.
 (2)  Modelling repressor proteins docking to DNA.
 Aloy P, Moont G, Gabb HA, Querol E, Aviles FX, Sternberg MJ
 Proteins. 1998 Dec 1;33(4):535-49.
 (3) Monte Carlo docking of protein-DNA complexes: incorporation of DNA
 flexibility and
      experimental data.
 Knegtel RM, Boelens R, Kaptein R
 Protein Eng. 1994 Jun;7(6):761-7.
 (4) A method for biomolecular structural recognition and docking
 allowing
 conformational
 flexibility.
 Sandak B, Nussinov R, Wolfson HJ
 J Comput Biol. 1998 Winter;5(4):631-54.
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 From: Armin M. Sobhani
 Just in case you want to know type of interactions, there is a good book
 that might be interesting:
 David M. J. Lilley (Ed.), (1995) DNA-Protein: Structural Interactions,
 IRL
 Press.
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