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Links tagged with 'protein structural homology'

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Found 59 links

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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

CaspRTool Content

http://igs-server.cnrs-mrs.fr/Caspr/index.cgi

Protein > 3-D Structure Prediction

CaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model.

NAR Web Server Issue 2004
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tagsescherichia coli proteins molecular models protein sequence analysis protein structural homology sequence alignment

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

COLORADO-3DTool Content

http://asia.genesilico.pl/colorado3d/

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

COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.

NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence color conserved sequence molecular models protein conformation protein structural homology

COMPASSTool Content

http://prodata.swmed.edu/compass/compass.php

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.

NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsamino acid motifs amino acid sequence amino acid sequence homology capsid proteins clathrin computational biology mamastrovirus molecular evolution molecular models molecular sequence data protein conformation protein databases protein structural homology proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical data interpretation statistics as topic tertiary protein structure trna methyltransferases

CPHmodels-3.0Tool Content

http://www.cbs.dtu.dk/services/CPHmodels/

Protein > 3-D Structure Prediction

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling.

NAR Web Server Issue 2010
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tagsalgorithms protein folding protein sequence analysis protein structural homology reproducibility of results

CSpritzTool Content

http://protein.bio.unipd.it/cspritz/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

CSpritz is a web server for the prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.

This content is being maintained by silvio.tosatto@unipd.it.

NAR Web Server Issue 2011
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tagsamino acid motifs molecular sequence annotation protein conformation protein structural homology secondary protein structure

Dali serverDatabase Content

http://ekhidna.biocenter.helsinki.fi/dali_server

Protein > 3-D Structure Comparison

The Dali server compares newly solved structures against structures in the PDB, allows browsing of pre-computed structural neighborhoods and generates suboptimal alignments from pairwise structure comparisons.

NAR Web Server Issue 2010
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tagsbacterial proteins protein databases protein sequence analysis protein structural homology

deconSTRUCTDatabase Content

http://epsf.bmad.bii.a-star.edu.sg/struct_server.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction

deconSTRUCT web server interfaces with a protein database search engine and can be used for the detection of similar protein (sub)structures.

This content is being maintained by ivanam.

NAR Web Server Issue 2010
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tagsalgorithms binding sites databases fold similariy molecular models protein databases protein structural homology protein structure comparison proteins secondary protein structure sub-structure