> > 3-D Structure Prediction

3-D Structure Prediction

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

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Found 97 links

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(PS)2 Protein Structure Prediction ServerTool Content

http://ps2.life.nctu.edu.tw [open in a new window]

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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.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
(PS)2: protein structure prediction server200627
NAR Web Server Issue 2006
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tagsamino acid sequence consensus sequence molecular models protein conformation protein sequence analysis sequence alignment

3D-JuryTool Content

http://meta.bioinfo.pl/submit_wizard.pl [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.

links directory index: 775
TitlePublication YearGoogle Scholar Citation Count
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure2003115
3D-Jury: a simple approach to improve protein structure predictions2003592
Detection of reliable and unexpected protein fold predictions using 3D-Jury200368
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology computer simulation database management systems humans molecular models protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment tertiary protein structure

3D-pssmTool Content

http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html [open in a new window]

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Protein > 3-D Structure Prediction

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

links directory index: 1748
TitlePublication YearGoogle Scholar Citation Count
Enhanced genome annotation using structural profiles in the program 3D-PSSM20001568
CAFASP-1: critical assessment of fully automated structure prediction methods1999180
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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/ [open in a new window]

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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.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes200914
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 [open in a new window]

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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
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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 [open in a new window]

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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.

This content is being maintained by Marc Delarue.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models20112
NAR Web Server Issue 2011
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tagsmolecular models protein conformation small angle scattering x-ray diffraction

ArchPredTool Content

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

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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
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tagsalgorithms molecular models protein conformation

AS2TSTool Content

http://as2ts.llnl.gov/ [open in a new window]

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

The AS2TS (Amino acid Sequence to Tertiary Structure) system consists of servers for protein structure analysis and modelling.

links directory index: 410
TitlePublication YearGoogle Scholar Citation Count
AS2TS system for protein structure modeling and analysis200524
LGA: A method for finding 3D similarities in protein structures2003386
NAR Web Server Issue 2003NAR Web Server Issue 2005
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tagsalgorithms biomolecular nuclear magnetic resonance proteins sequence alignment

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/ [open in a new window]

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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.

This content is being maintained by kimmen.

links directory index: 4963
TitlePublication YearGoogle Scholar Citation Count
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis200720
MUSCLE: multiple sequence alignment with high accuracy and high throughput20044855
SATCHMO: sequence alignment and tree construction using hidden Markov models200388
Phylogenetic inference in protein superfamilies: analysis of SH2 domains.19980
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/ [open in a new window]

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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
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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/ [open in a new window]

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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.

links directory index: not available
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BioverseTool Content

http://bioverse.compbio.washington.edu/ [open in a new window]

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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.

links directory index: 95
TitlePublication YearGoogle Scholar Citation Count
Functional annotation from predicted protein interaction networks200537
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes200513
Enhanced functional information from predicted protein networks200420
Bioverse: Functional, structural and contextual annotation of proteins and proteomes200325
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 [open in a new window]

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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.

links directory index: 71
TitlePublication YearGoogle Scholar Citation Count
CaspR: a web server for automated molecular replacement using homology modelling200471
NAR Web Server Issue 2004
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COLORADO-3DTool Content

http://asia.genesilico.pl/colorado3d/ [open in a new window]

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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.

links directory index: 50
TitlePublication YearGoogle Scholar Citation Count
COLORADO3D, a web server for the visual analysis of protein structures200450
NAR Web Server Issue 2004
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CPHmodels-3.0Tool Content

http://www.cbs.dtu.dk/services/CPHmodels/ [open in a new window]

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Protein > 3-D Structure Prediction

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

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles201037
NAR Web Server Issue 2010
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tagsalgorithms protein folding protein sequence analysis protein structural homology reproducibility of results

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