Local backbone structure prediction of proteins.
A statistical analysis of the PDB structures has led us to define a new set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one is defined by the (phi, psi) dihedral angles of 5 consecutive residues. The amino acid distributions observed in sequence windows encompassing these PBs are used to predict by a Bayesian approach the local 3D structure of proteins from the sole knowledge of their sequences. LocPred is a software which allows the users to submit a protein sequence and performs a prediction in terms of PBs. The prediction results are given both textually and graphically.
de Brevern
Alexandre G
AG
Equipe de Bioinformatique Génomique et Moléculaire, INSERM E03-46, Université Denis Diderot - Paris 7, 75251 Paris, France. alexandre.debrevern@ebgm.jussieu.fr
Benros
Cristina
C
Gautier
Romain
R
Valadié
Héléne
H
Hazout
Serge
S
Etchebest
Catherine
C
D000595:Amino Acid Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins
Proteins. 2000 Nov 15;41(3):271-87
11025540
Proteins. 2002 May 1;47(2):228-35
11933069
Bioinformatics. 2002;18 Suppl 1:S54-61
12169531
Protein Sci. 2002 Dec;11(12):2871-86
12441385
Bioinformatics. 2003 Feb 12;19(3):345-53
12584119
BMC Bioinformatics. 2004 May 12;5:58
15140270
Proteins. 2000 Oct 1;41(1):17-20
10944389
J Mol Biol. 1998 Aug 21;281(3):565-77
9698570
J Mol Biol. 1999 Sep 17;292(2):195-202
10493868
Trends Biochem Sci. 1995 Sep;20(9):374
7482707
Bioinformatics. 2000 Apr;16(4):404-5
10869041
J Mol Biol. 2000 Aug 4;301(1):173-90
10926500