> > 3-D Structure Comparison

3-D Structure Comparison

Resources for the comparison of sequences at the level of tertiary structure are also found here. This includes tools for superimposing structures and for creating structural alignments.

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Displaying 15 links

3D-FunTool Content

http://3dfun.bioinfo.pl

Protein > 3-D Structure Comparison
Protein > Annotation and Function

3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.

NAR Web Server Issue 2008
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tagsalgorithms enzymes molecular models protein structural homology

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

3DSSTool Content

http://cluster.physics.iisc.ernet.in/3dss/options.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

3-Dimensional Structural Superposition (3DSS) is a tool for superposing two or more protein structures that uses RASMOL for visualization; some browser configuration is necessary.

NAR Web Server Issue 2006
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tagsmolecular models phospholipases a protein databases protein structural homology water

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

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

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

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

CATHDatabase Content

http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H).

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tagsamino acid sequence homology animals automation genomics protein databases protein folding protein structural homology proteins secondary protein structure tertiary protein structure

CE-MCTool Content

http://bioinformatics.albany.edu/~cemc/

Protein > 3-D Structure Comparison
Sequence Comparison > Multiple Sequence Alignments

A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.

NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence amino acid sequence homology aspartic acid endopeptidases factual databases molecular sequence data monte carlo method protein kinases proteins secondary protein structure sequence alignment software design

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

CLICKTool Content

http://mspc.bii.a-star.edu.sg/click

Protein > 3-D Structure Comparison

CLICK web server is a topology independent method of comparison of biomolecular 3D structures.

NAR Web Server Issue 2011
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Combinatorial Extension of the Optimal PathDatabase Content

http://cl.sdsc.edu/ce.html

Protein > 3-D Structure Comparison

Calculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank.

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tagsalgorithms amino acid sequence amino acid sequence homology molecular sequence data monte carlo method protein conformation protein folding proteins sequence alignment

ConPlexTool Content

http://sbi.postech.ac.kr/ConPlex/

Protein > 3-D Structure Comparison

ConPlex is a web server that enables conservation analyses of protein interactions within protein quaternary structures. Results of the residue specific conservation analysis are displayed on the input protein complex structure.

NAR Web Server Issue 2010
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tagsamino acid sequence homology molecular evolution multiprotein complexes quaternary protein structure

COPSTool Content

http://cops.services.came.sbg.ac.at/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.

NAR Web Server Issue 2009
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tagsmolecular models protein databases protein folding proteins tertiary protein structure

Tags associated with subcategory 'Protein/3-D Structure Comparison'

proteins protein databases molecular models protein structural homology protein conformation algorithms sequence alignment protein sequence analysis amino acid sequence amino acid sequence homology protein folding computational biology binding sites molecular sequence data tertiary protein structure factual databases animals secondary protein structure ligands ovomucin plant proteins online systems plant lectins systems integration protein binding transcription factors automated pattern recognition chemical models software validation x-ray crystallography protein interaction mapping quaternary protein structure recombinant proteins lectins molecular structure color conserved sequence enzyme inhibitors chymotrypsin beetles normal distribution time factors amino acids fabaceae genetic databases cluster analysis medicinal plants molecular cloning hydrogen bonding hiv integrase nucleic acids sequence analysis sequence homology proteasome endopeptidase complex database management systems genes genetic models fibronectins evaluation studies as topic consensus sequence dna dna sequence analysis humans messenger rna aspartic acid endopeptidases monte carlo method protein kinases sensitivity and specificity rna sequence analysis phylogeny protein-serine-threonine kinases reproducibility of results computer simulation base sequence statistical models structure-activity relationship probability peptide mapping genome globins peptide library software design proprotein convertases drug design integrins macromolecular substances trypsin inhibitors potassium channels protein tyrosine phosphatases markov chains molecular evolution molecular conformation zinc fingers s-phase kinase-associated proteins hemoglobins molecular dynamics simulation protein interaction domains and motifs erythropoietin receptors sub-structure heterotrimeric gtp-binding proteins drug discovery