MolSurfer:
a Macromolecular Interface Navigator - is a Java-based program
which can be used to study
protein-protein and protein-DNA/RNA
interfaces. The 2D
projections of the computed interface aid
visualization of
complicated interfacial
geometries in 3D. Molecular
properties,
including hydrophobicity and electrostatic potential,
can be projected onto the interface. MolSurfer can thereby aid
exploration
of molecular complementarity, identification
of binding "hot
spots" and prediction of the effects
of mutations.
MolSurfer can also
facilitate the location of cavities
at macromolecular interfaces. (Reference: R.R. Gabdoulline
et al. (1999) Trends Biochem. Sci.,
24:
285-287)
PQS Protein
Quaternary Structure (EMBL-EBI)
InterPreTS prediction - combines three-dimensional
information of protein complexes, from their database of
interacting domains, with an empirical scoring system to assess the fit of
any potential protein interacting pair with a
known three-dimensional structure. (Reference:
P. Aloy & R.B. Russell (2003) Bioinformatics. 19, 161-162).
STRING - a Search Tool for the Retrieval of Interacting Genes/Proteins
- Associations are derived from high-throughput
experimental data, mining databases and literature, and from
predictions based on genomic context analysis. STRING integrates and ranks
these associations by benchmarking them against a common reference set,
and presents evidence in a consistent and intuitive web interface.
Importantly, the associations are extended beyond the organism in which
they were originally described, by automatic transfer to orthologous
protein pairs in other organisms, where applicable. (Reference:
C. von Mering et al. 2005. Nucleic Acids Research
33 (Database issue):
D433-7).
meta-PPISP is built
on three individual web servers: cons-PPISP,
PINUP, and Promate. This is a meta web server for protein-protein
interaction site prediction.(Reference: Qin, S.B.
& Zhou, H.-X. 2007. Bioinformatics 23:
3386-3387)