PFRMAT AL 
TARGET T0074 
AUTHOR 3873-9906-1225 
REMARK Submission 2 
REMARK Work by Gidon Moont (1) , Lawrence Kelley (1), 
REMARK Bob MacCallum (1), Marcel Turcotte (1) Mansoor Saqi (2) 
REMARK and Michael Sternberg (1) (m.sternberg@icrf.icnet.uk) 
REMARK (1) Biomolecular Modelling Laboratory, 
REMARK Imperial Cancer Research Fund 
REMARK (1) Lincoln's Inn Fields, London WC2A 3PX, UK 
REMARK (2) Bioinformatics Group, GlaxoWellcome, Stevenage, UK 
METHOD 
METHOD Method outline 
METHOD --------------- 
METHOD unknown = target, library of known folds = template 
METHOD (0) Initial check for remote homology of target 
METHOD to templates of known structures using PSI-BLAST 
METHOD (1) Secondary structure & sequence target against fold 
METHOD template library using FOLDFIT 
METHOD (2) Multiple structure / multiple sequence matching 
METHOD  against fold template library (3D-PSSM) *** NEW METHOD*** 
METHOD (3) Search against Hidden Markov Models for fold template 
METHOD library using SAM 
METHOD (4) Local hydrophobicity and predicted secondary structure 
METHOD matched for target and template using SIVA (MacCallum & 
METHOD Thornton) 
METHOD (6) Evaluation of above results in terms of literature and 
METHOD function of target. 
METHOD 
METHOD General features of approach 
METHOD ----------------------------- 
METHOD 
METHOD (i) The fold (template) library consists of non-redundant 
METHOD SCOP domains with <40% sequence identity per family (called 
METHOD SCOP40). 
METHOD 
METHOD (ii) Secondary structure prediction from multiple alignment 
METHOD (homologues gathered with PSI-BLAST) DSC (King & 
METHOD Sternberg); PHD (Rost & Sander); JPRED (Barton) 
METHOD 
METHOD Method details 
METHOD -------------- 
METHOD 
METHOD (1) FOLDFIT (Russell,R.B., Saqi, M.A.S., Bates,P.A., 
METHOD Sayle,R.A.  & Sternberg, M.J.E. (1998). Prot Eng 11, 1-9.) 
METHOD The target is represented by sequence and predicted 
METHOD secondary structure and scanned against known secondary 
METHOD structure and sequence for template in fold library. 
METHOD Different weights for secondary structure and sequence are 
METHOD used to obtain different possible top hits. 
METHOD 
METHOD (2) 3D-PSSM - Structures within the same SCOP fold family 
METHOD are aligned in 3D and if structures can be superposed well 
METHOD then each is used together with all homologous 
METHOD sequences in sequence database found by PSI-BLAST. 
METHOD These 3D-PSSMs were generated for each template. 
METHOD The target is matched against each template, 
METHOD (3D-PSSM, Kelley, MacCallum, Saqi & Sternberg, unpublished). 
METHOD NOW INCLUDING PREDICTED SECONDARY STRUCTURE 
METHOD as in FOLDFIT. 
METHOD 
METHOD (3) HMM from SAM (Hughley & Krogh ) against a 
METHOD library generated from each 
METHOD template in SCOP40 (Moont, MacCallum & Sternberg). 
METHOD 
METHOD (4) Vector-based alignment of per-residue hydrophobicity 
METHOD and DSC predicted secondary structure probabilities for 
METHOD both target and template. This approach could also 
METHOD be used in the absence of known structures for library 
METHOD sequences.  Algorithm is SIVA (MacCallum & Thornton, 
METHOD unpublished) 
METHOD 
METHOD 
METHOD (5) Visual inspection of results. 
METHOD 
METHOD details for t0074 
METHOD PSIBLAST, FOLDFIT, SIVA, 3DPSSM all identify 
METHOD the e-f hand proteins as top hit 
METHOD Automatic alignments with minor adjustement 
METHOD used to generate model 
MODEL 1 
PARENT 1osa 
E  127 E 7 
D  128 Q 8 
K  129 I 9 
A  130 A 10 
K  131 E 11 
Y  132 F 12 
D  133 K 13 
A  134 E 14 
I  135 A 15 
F  136 F 16 
D  137 A 17 
S  138 L 18 
L  139 F 19 
G  144 G 25 
F  145 T 26 
L  146 I 27 
S  147 T 28 
G  148 T 29 
D  149 K 30 
K  150 E 31 
V  151 L 32 
K  152 G 33 
P  153 T 34 
V  154 V 35 
L  155 M 36 
L  156 R 37 
K  159 N 42 
L  160 P 43 
P  161 T 44 
V  162 E 45 
D  163 A 46 
I  164 E 47 
L  165 L 48 
G  166 Q 49 
R  167 D 50 
V  168 M 51 
W  169 I 52 
E  170 N 53 
L  171 E 54 
S  172 V 55 
D  173 D 56 
I  174 A 57 
D  175 D 58 
H  176 G 59 
D  177 N 60 
G  178 G 61 
M  179 T 62 
L  180 I 63 
D  181 D 64 
R  182 F 65 
D  183 P 66 
E  184 E 67 
F  185 F 68 
TER 
END 
