Dear All,
Thanks to all that replied in private and in the bb!
Answers are and will be 'permanently' summarized at:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Mapping_sequence_alignment_to_a_structure
(a nice opportunity to create a missing chapter!)
Tassos
On 29 Jan 2009, at 22:39, Luca Jovine wrote:
On 29 Jan 2009, at 22:25, Anastassis Perrakis wrote:
Dear all,
I was wondering what is the state of the art for this old dark
art ... are there any good servers / programs that allow to easily
upload your own sequence alignments or create a 'transparent'
alignment (I want to see the alignment first and not a total black
box) and then allow you to write out sequence conservation based
either on identity or in e.g a Dayhoff matrix on the B factor column
for displaying it later in eg Pymol?
To be clear I do not want a structural alignment, but mapping
sequence alignment of eg a family to a single structure of a family
member.
Thanks in advance, Tassos
Hi Tassos,
Consurf will do the job! Have a look at:
http://consurf.tau.ac.il
HTH,
Luca
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Luca Jovine, Ph.D.
Group Leader, Protein Crystallography Unit
Karolinska Institutet
Department of Biosciences and Nutrition
Hälsovägen 7, SE-141 57 Huddinge, Sweden
Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org
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