> > 3-D Structural Features

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.

RSS Feed Compact View Sort by Links Directory Index
downloadList as XML List as JSON List as TSV List as CSV
Hide Resources (2)Hide Databases (5)Hide Tools (111)

Found 118 links

Displaying 15 links

3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/ [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > Networks & Interactions, Pathways and Enzymes

3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
3D-partner: a web server to infer interacting partners and binding models200727
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence amino acid sequence homology binding sites gene expression profiling molecular sequence data protein binding protein databases protein interaction mapping protein sequence analysis proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins tertiary protein structure

3DLigandSiteTool Content

http://www.sbg.bio.ic.ac.uk/3dligandsite [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Molecular Dynamics and Docking

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.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
3DLigandSite: predicting ligand-binding sites using similar structures201021
NAR Web Server Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

links directory index: 98
TitlePublication YearGoogle Scholar Citation Count
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures20073
Query3d: a new method for high-throughput analysis of functional residues in protein structures200536
A structural study for the optimisation of functional motifs encoded in protein sequences20047
Three-dimensional profiles: a new tool to identify protein surface similarities199852
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

3DTFTool Content

http://cogangs.biobase.de/3dtf/ [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > Molecular Dynamics and Docking

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
NAR Web Server Issue 2012
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0

3VTool Content

http://3vee.molmovdb.org [open in a new window]

Share This Link
Protein > 3-D Structural Features

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.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
3V: cavity, channel and cleft volume calculator and extractor201011
NAR Web Server Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0

ALADYNTool Content

http://aladyn.escience-lab.org [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

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.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ALADYN: a web server for aligning proteins by matching their large-scale motion20106
NAR Web Server Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamyloid precursor protein secretases cysteine endopeptidases exodeoxyribonucleases hiv protease motion protein conformation protein structural homology proteins

AnalyCysDatabase Content

http://bioinformatics.univ-reunion.fr/analycys/ [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

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
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0

ANCHORTool Content

http://structure.pitt.edu/anchor [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > Networks & Interactions, Pathways and Enzymes

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

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery201012
NAR Web Server Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

links directory index: 627
TitlePublication YearGoogle Scholar Citation Count
Tools for comparative protein structure modeling and analysis2003190
Modeller: generation and refinement of homology-based protein structure models2003437
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

ArchPredTool Content

http://manaslu.aecom.yu.edu/loopred/ [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

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
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms molecular models protein conformation

BhairPredTool Content

http://www.imtech.res.in/raghava/bhairpred/ [open in a new window]

Share This Link
Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.

This content is being maintained by raghavagps.

links directory index: 45
TitlePublication YearGoogle Scholar Citation Count
BhairPred: prediction of beta-hairpins in a protein from multiple alignment information using ANN and SVM techniques200545
NAR Web Server Issue 2005
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms artificial intelligence neural networks (computer) protein sequence analysis secondary protein structure sequence alignment

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/ [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Molecular Dynamics and Docking
Protein > Networks & Interactions, Pathways and Enzymes

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.

This content is being maintained by BioInfo3D.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
BioInfo3D: a suite of tools for structural bioinformatics200424
NAR Web Server Issue 2004
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

BioMeTool Content

http://metals.zesoi.fer.hr [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > Biochemical Features

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
NAR Web Server Issue 2012
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0

BSDDDatabase Content

http://iris.physics.iisc.ernet.in/bsdd/ [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.

This content is being maintained by kitty.pillai.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BSDD: Biomolecules Segment Display Device--a web-based interactive display tool20041
NAR Web Server Issue 2004
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid motifs molecular models molecular structure proteins

CAPS-DBDatabase Content

http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Databases

CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. CASP-DB is fully browsable and searchable and is regularly updated.

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
CAPS-DB: a structural classification of helix-capping motifs.20120
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0

Associated Tag Cloud