SNPs&GO

SNPs&GO^3d
Predicting disease associated variations using GO terms

PDB File: pdb1cdf.spdb Chain: A
Alignment File: pdb1cdf.spdb.blast
GO-terms File: pdb1cdf.spdb.seq.go
Output File: output.txt

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Jmol Version: 13.1.10_dev $Date: 2012-12-05 21:20:15 -0600 (Wed, 05 Dec 2012) $

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1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

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RECEPTOR 26-MAR-96 1CDF

THREE-DIMENSIONAL THEORETICAL MODEL OF THE LIGAND BINDING

DOMAIN OF THE HUMAN B CELL RECPTOR CD40

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Mutation	Prediction	RI	Probability	Method

C26Q	Disease	7	0.828	S3D-PROF: F[C]=100% F[Q]=0% Nali=51 RSA=8
	Disease	8	0.887	PANTHER: F[C]=80% F[Q]=0%
	Disease	9	0.925	SNPs&GO
	Disease	9	0.960	S3Ds&GO

C83R	Disease	8	0.880	S3D-PROF: F[C]=100% F[R]=0% Nali=87 RSA=14
	Disease	10	0.977	PANTHER: F[C]=94% F[R]=0%
	Disease	10	0.975	SNPs&GO
	Disease	9	0.970	S3Ds&GO

S124L	Neutral	9	0.048	S3DPROF: F[S]=10% F[L]=8% Nali=85 RSA=86
	Neutral	8	0.106	PANTHER: F[S]=10% F[L]=15%
	Neutral	6	0.184	SNPs&GO
	Neutral	5	0.231	S3Ds&GO

Mutation: WT+POS+NEW
    WT: Residue in wild-type protein
    POS: Residue position
    NEW: New residue after mutation

Prediction:
    Neutral: Neutral variation
    Disease: Disease associated variation

RI: Reliability Index

Probability: Disease probability (if >0.5 mutation is predicted Disease)

Method: SVM type and data
    PANTHER: Output of the PANTHER algorithm
    S3D-PROF: SVM input is the protein structure and profile at the mutated position
    SNPs&GO: Standard sequence-based SNPs&GO method.
    S3Ds&GO: SVM input is all the input in S3D-PROF, PANTHER and GO terms

F[X]: Frequency of residue X in the sequence profile
Nali: Number of aligned sequences in the mutated site
RSA: Relative Solvent Accesible Area