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)
PDBePISA (Protein Interfaces, Surfaces and Assemblies) - is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters.
The STRING (Search Tool for Recurring Instances of Neighbouring Genes) database aims to provide a critical assessment and integration of protein–protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10.0 of STRING covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein–protein associations from co- expression data. (Reference: D. Szklarczyk et al. 2015. Nucl. Acids Res. 43 (D1): D447-D452).
AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures. The identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. (Reference: R. Zambrano et al. 2015. Nucl. Acids Res. 43 (W1): W306-W313.
NPDock ((Nucleic acid–Protein Docking) - a novel web server for predicting complexes of protein–nucleic acid structures which implements a computational workflow that includes docking, scoring of poses, clustering of the best-scored models and refinement of the most promising solutions. The NPDock server provides a user-friendly interface and 3D visualization of the results. (Reference: I. Tuszynska et al. 2015. Nucl. Acids Res. 43 (W1): W425-W430).
STITCH (Search Tool for Interactions of Chemicals) - is a database of protein–chemical interactions that integrates many sources of experimental and manually curated evidence with text-mining information and interaction predictions (Reference: Kuhn, M. et al. 2014. Nucl. Acids Res. 42 (D1): D401-D407).
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)
QuatIdent: identifying the quaternary structural attribute of a protein chain based on its sequence (Reference: Shen H-B & Chou K-C. 2009. J Proteome Res. 8: 1577-1584).
LigDig - is a web server designed to answer questions that previously required several independent queries to diverse data sources. It is modular in design and consists of seven tools, which can be used separately, or via linking the output from one tool to the next. These allow a user to: (i) perform a free- text compound search, (ii) search for suitable ligands, particularly inhibitors, of a protein and query their interaction network, (iii) search for the likely function of a ligand, (iv) perform a batch search for compound identifiers, (v) find structures of protein-ligand complexes, (vi) compare three- dimensional structures of ligand binding sites and (vii) prepare coordinate files of protein-ligand complexes for further calculations. (Reference: Fuller JC et al. 2015. Bioinformatics 31:1147-1149).
14-3-3-Pred: A webserver to predict 14-3-3-binding phosphosites in human proteins (Reference: Madeira F et al. 2015. Bioinformatics 31: 2276-2283).