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3-D Structure Prediction

This section contains links to resources to aid in protein 3D structure prediction.

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Found 79 links

Displaying 15 links

(PS)2 Protein Structure Prediction ServerTool Content

http://ps2.life.nctu.edu.tw

Protein > 3-D Structure Prediction

(PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T-Coffee for template selection and target-template alignment. The final three-dimensional (3D) structure is built using RAMP or MODELLER.

NAR Web Server Issue 2006
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tagsamino acid sequence consensus sequence molecular models protein conformation protein sequence analysis sequence alignment

3D-pssmTool Content

http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html

Protein > 3-D Structure Prediction

Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome bacterial proteins computational biology factual databases flavoproteins integrases molecular models molecular sequence data mycoplasma open reading frames protein folding proteins proteome reproducibility of results retroviridae proteins ribonuclease h secondary protein structure sequence alignment solvents structure-activity relationship

@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

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

AquaSAXSTool Content

http://lorentz.dynstr.pasteur.fr/aquasaxs.php

Protein > 3-D Structure Prediction

AquaSAXS is a web server for computation of and fitting of small angle x-ray scattering (SAXS) profiles with non-uniformally hydrated atomic models.

NAR Web Server Issue 2011
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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

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

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

Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/

DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Localization and Targeting
Protein > Molecular Dynamics and Docking
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

NAR Web Server Issue 2005NAR Web Server Issue 2003
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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

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

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

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

CS23DTool Content

http://www.cs23d.ca

Protein > 3-D Structure Prediction

Chemical Shift to 3D Structure (CS23D) generates accurate 3D protein structures using only NMR chemical shifts and sequence data. Output is a set of PDB coordinates for the protein.

NAR Web Server Issue 2008
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tagsalgorithms biomolecular nuclear magnetic resonance protein conformation protein databases protein sequence analysis

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

molecular models protein conformation proteins protein sequence analysis algorithms protein databases sequence alignment protein folding reproducibility of results computational biology secondary protein structure amino acid sequence amino acid sequence homology tertiary protein structure molecular sequence data protein structural homology humans computer simulation animals point mutation nucleic acids molecular conformation protein binding ribonucleotides ricin transcription factors proteomics site-directed mutagenesis serpins protein interaction mapping automated pattern recognition cluster analysis globins database management systems programming languages molecular structure water streptavidin protein engineering ligands interferon alfa-2a crystallography papain hydrogen bonding false positive reactions fungal genome london membrane proteins capsid proteins single nucleotide polymorphism sulfites temperature ultraviolet rays nucleic acid conformation mutation neural networks (computer) peptide fragments gene expression regulation signal transduction porins formycins biotin energy metabolism peptide library polypyrimidine tract-binding protein aspartic acid endopeptidases calmodulin hydroxymethylbilane synthase documentation phylogeny peptide mapping genome online systems bacterial genome bacterial proteins chemical models artificial intelligence tissue kallikreins trichomonas vaginalis trypsin tissue plasminogen activator thermodynamics flavoproteins integrases ribonuclease h solvents structure-activity relationship systems integration switzerland retroviridae proteins proteome automation factual databases conserved sequence open reading frames mycoplasma theoretical models sequence homology normal distribution sensitivity and specificity src homology domains