HELP CONTENTS:

I.  PolyPhen Overview
I.1.  Sequence-based characterisation of the substitution site
I.2.  Calculation of PSIC profile scores for two amino acid variants
I.3.  Calculation of structural parameters and contacts
I.3.1. Mapping of the substitution site to known protein 3D structures
I.3.2. Structural parameters
I.3.2.1. Parameters taken from DSSP
I.3.2.2. Calculated parameters
I.3.3. Contacts
I.3.3.1. Contacts with heteroatoms
I.3.3.2. Interchain contacts
I.3.3.3. Contacts with functional sites

II.  Prediction
II.1.  Prediction rules
II.2.  Available data
II.2.  Prediction basis
II.3.  Substitution effect

III.  PolyPhen input
III.1.  Query data
III.2.  Options

IV.  PolyPhen output
IV.1.  Query
IV.2.  Prediction
IV.3.  Details
IV.3.1. Sequence features of the substitution site
IV.3.2. PSIC profile scores for two amino acid variants
IV.3.3. Structural parameters and contacts
IV.3.3.1. Mapping of the substitution site to known protein 3D structures
IV.3.3.2. Structural parameters
IV.3.3.3. Contacts

V.  PolyPhen SNP data collection
V.1.  Mapping known human SNPs to genes
V.2.  Data collection statistics
V.3.  Data collection search
V.4.  Data collection format