Interface Analysis
PIPSA service is provided for the comparison of the electrostatic interaction properties of proteins. It permits the classification of proteins according to their interaction properties.
http://pipsa.eml.org/pipsa/pipsa-index.jsp
PDBePISA 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.
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
Multiple Alignment of Protein-Protein InterfaceS recognizes spatially conserved chemical interactions shared by a set of protein-protein interfaces.
http://bioinfo3d.cs.tau.ac.il/MAPPIS/
Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites.
http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/index.html
The PROTORP server is a bioinformatics tool designed to analyse the interfaces between protein chains in protein-protein associations.
http://www.bioinformatics.sussex.ac.uk/protorp/
A Macromolecular Interface Navigator. MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. MolSurfer 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.
http://projects.villa-bosch.de/dbase/molsurfer/
A server for the analysis of the physicochemical features of protein-protein interfaces.
http://resources.boseinst.ernet.in/resources/bioinfo/interface/
AquaProt analyses protein-protein binding interface, defines inter-residue interaction map within the interface and extracts related water molecules.
http://bioinfo.weizmann.ac.il/aquaprot/
VASCo is a program pipeline including a visualization tool to calculate and visualize annotated surfaces with special emphasis on surface contact regions and protein-protein interactions.
http://genome.tugraz.at/VASCo/
LIGPLOT Automatically generates schematic diagrams of protein-ligand interactions for a given PDB file.
http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/
Ligand-Protein Contacts & Contacts of Structural Units
http://bip.weizmann.ac.il/oca-bin/lpccsu
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