Table 1

Servers evaluated in this work

Server name

Method type

Training dataset

Reference


CEP (Conformational Epitope Prediction)

Discontinuous epitope prediction based on residue solvent accessibility and spatial distribution.

No training set.

[48]

DiscoTope

Discontinuous epitope prediction based on amino acid statistics, residue solvent accessibility and spatial distribution.

75 structures of antibody-antigen complexes.

[49]

ProMate

Protein-protein binding interface prediction based on significant structural and sequence interface properties.

Manually curated; 57 protein involved in heterodimeric transient interactions (excluding antigen-antibody complexes).

[55]

PIER (Protein IntErface Recognition)

Protein-protein binding interface prediction based on local statistical properties of the protein surface derived at the level of atomic groups.

490 homodimeric, 62 heterodimeric and 196 transient interfaces (excluding antigen-antibody complexes).

[54]

PPI-PRED (Protein-Protein Interface Prediction)

Protein-protein binding interface prediction based on significant structural and sequence interface properties.

Manually curated; 180 proteins from 149 complexes both obligate (114) and transient (66).

[53]

ConSurf

Mapping of phylogenetic information (sequence conservation grades) on to the surface of proteins with known 3D structure.

No training set.

[56]

ClusPro (DOT program)

Rigid-body protein-protein docking based on the Fast-Fourier Transform correlation approach.

No training set.

[50] [51]

PatchDock

Rigid-body protein-protein docking based on local shape feature matching.

No training set.

[52]


Ponomarenko and Bourne BMC Structural Biology 2007 7:64   doi:10.1186/1472-6807-7-64

Open Data