3-D Structural Features

This section includes tools for searching for structural motifs, biochemical features found in protein structures, and functional sub-structures such as binding sites.

Found 124 links

Displaying 15 links

3DEM LoupeTool Content

Share This Link

3DEM Loupe is a web-server that allows normal mode analysis of any uploaded electron microscopy volume. Results can be explored in 3 dimensions through animations and movies.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

3DLigandSiteTool Content

Share This Link

3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.

3DTFTool Content

Share This Link

3D Transcription Factor (3DTF) is a web-server for the analysis of protein-DNA binding sites. It calculates the positional weight matrix (PWM), representing the DNA-binding specifity of the protein.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

3VTool Content

Share This Link

The 3V web server extracts and analyzes all of the internal volumes from input RNA and protein structures. Output is volumetric representations in images and downloadable files.

AdepthTool Content

Share This Link

Adepth web server provides both depth and height representation of an atom in a macromolecule; it is capable of computing isosurfaces for atomic depths and presenting graphical view of marcomolecular shape at some distance away from the surface.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

ALADYNTool Content

Share This Link

The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.

AnalyCysDatabase Content

Share This Link

AnalyCys is database for the analysis of conservation and conformation of disulphide bonds in SCOP structural families. This database has a wide range of applications including mapping of disulphide bond mutation patterns, identification of cysteine residues and disulphide bonds important for folding and stabilization, modeling of protein structures and in protein engineering.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

ANCHORTool Content

Share This Link

ANCHOR is a web-based tool for the analysis of protein-protein interfaces. ANCHOR indicates possible druggable pockets within the protein using anhor residues.

ArchPredTool Content

Share This Link

ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
ArchPRED: a template based loop structure prediction server200626

BioMeTool Content

Share This Link

Biologically Relevant Metals (BioMe) is a web based platform for calculation of various statistical properties of metal binding sites including distribution of coordinate geometry and other descriptive statistics for a metal ion. The underlying database contains for each metal ion: PDB code, structure determination method, types of metal binding chains and names and coordinates of bound ligands, among other details.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

Associated Tag Cloud