> > 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.

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3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

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

NAR Web Server Issue 2007
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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

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.

NAR Web Server Issue 2010
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tagsalgorithms binding sites ligands molecular models protein sequence analysis protein structural homology reproducibility of results

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html

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.

NAR Web Server Issue 2007
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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

3VTool Content

http://3vee.molmovdb.org

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.

NAR Web Server Issue 2010
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tagsbinding sites molecular models nucleic acid conformation protein conformation rna

ALADYNTool Content

http://aladyn.escience-lab.org

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.

NAR Web Server Issue 2010
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tagsamyloid precursor protein secretases cysteine endopeptidases exodeoxyribonucleases hiv protease motion protein conformation protein structural homology proteins

AnalyCysDatabase Content

http://bioinformatics.univ-reunion.fr/analycys/

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.

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ANCHORTool Content

http://structure.pitt.edu/anchor

Protein > 3-D Structural Features
Protein > Interactions, Pathways, 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.

NAR Web Server Issue 2010
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tagsbinding sites drug discovery multiprotein complexes protein databases protein interaction mapping

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml

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).

NAR Web Server Issue 2003
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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/

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.

NAR Web Server Issue 2006
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tagsalgorithms molecular models protein conformation

BhairPredTool Content

http://www.imtech.res.in/raghava/bhairpred/

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.

NAR Web Server Issue 2005
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tagsalgorithms artificial intelligence neural networks (computer) protein sequence analysis secondary protein structure sequence alignment

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

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.

NAR Web Server Issue 2004
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tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

BSDDDatabase Content

http://iris.physics.iisc.ernet.in/bsdd/

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.

NAR Web Server Issue 2004
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tagsamino acid motifs molecular models molecular structure proteins

CASTpTool Content

http://sts.bioengr.uic.edu/castp/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

NAR Web Server Issue 2003NAR Web Server Issue 2006
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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

CCRXPTool Content

http://ccrxp.netasa.org

Protein > 3-D Structural Features
Protein > Sequence Features

A tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue clusters are also computed.

This content is being maintained by shandar.

NAR Web Server Issue 2010
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tagsclustered residues consensus sequence conservation score dna-binding proteins hot spots interface multiprotein complexes mutation proteins rna-binding proteins solvent accessibility

CHC_FINDTool Content

http://schubert.bio.uniroma1.it/CHC_FIND/index.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Sequence Comparison > Analysis of Aligned Sequences

CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.

NAR Web Server Issue 2005
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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

Tags associated with subcategory 'Protein/3-D Structural Features'

protein conformation proteins molecular models algorithms protein databases binding sites computational biology protein sequence analysis tertiary protein structure amino acid sequence protein structural homology amino acids protein folding ligands sequence alignment humans quaternary protein structure polysaccharide-lyases online systems recombinant proteins proteoglycans protein binding ovomucin plant lectins plant proteins sulfates systems integration bacterial genome x-ray crystallography gene expression profiling genetic databases genomics genome fungal genome false positive reactions mathematics london database management systems factual databases documentation iduronic acid polyacrylamide gel electrophoresis enzyme inhibitors fabaceae hiv integrase medicinal plants lectins computer simulation color protonation animals beetles chymotrypsin chemical models molecular cloning chondroitin lyases heparin lyase heparitin sulfate mammalian embryo multiprotein complexes molecular weight glycosaminoglycans glucuronic acid chromatography cultured cells dermatan sulfate glucuronates fibroblasts pliability membrane proteins ribonucleases single nucleotide polymorphism trypsin inhibitors amino acid substitution amino acid sequence homology theoretical models structural models molecular conformation programming languages solvents sequence homology static electricity molecular sequence data structure-activity relationship potassium channels proto-oncogene proteins c-bcl-2 sequence analysis conserved sequence molecular structure phylogeny nucleic acid conformation proteome macromolecular substances secondary protein structure molecular evolution bcl-x protein mathematical computing hydrogen bonding protein isoforms thermodynamics proteomics