> > 2-D Structure Prediction

2-D Structure Prediction

This sections contains links to several programs which predict protein secondary structure. A link to resources for the evaluation of protein structure prediction is also found here.

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Found 55 links

Displaying 15 links

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

BOMPTool Content

http://www.bioinfo.no/tools/bomp

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.

NAR Web Server Issue 2004
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tagsbacterial genome bacterial outer membrane proteins escherichia coli gram-negative bacteria protein sequence analysis salmonella typhimurium secondary protein structure

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

NAR Web Server Issue 2005
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tagsprotein sequence analysis systems integration

COILSTool Content

http://www.ch.embnet.org/software/COILS_form.html

Protein > 2-D Structure Prediction

Prediction of coiled coil regions.

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tagsamino acid sequence amino acids animals factual databases humans probability protein conformation proteins

DICHROWEBTool Content

http://dichroweb.cryst.bbk.ac.uk/html/home.shtml

Protein > 2-D Structure Prediction

A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.

NAR Web Server Issue 2004
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tagsalgorithms circular dichroism computational biology protein databases secondary protein structure

DisEMBLTool Content

http://dis.embl.de/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

A computational tool for prediction of disordered/unstructured regions within a protein sequence.

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tagscircular dichroism humans ligands magnetic resonance spectroscopy neural networks (computer) protein conformation proteins proteome sensitivity and specificity src homology domains statistics as topic temperature theoretical models ultraviolet rays x-ray crystallography

DSSPcontTool Content

http://cubic.bioc.columbia.edu/services/DSSPcont/

Protein > 2-D Structure Prediction

DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence biomolecular nuclear magnetic resonance hydrogen bonding molecular models proteins secondary protein structure

ENDscriptTool Content

http://espript.ibcp.fr/ESPript/ENDscript/index.php

Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology data display database management systems dna-binding proteins factual databases molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

EVATool Content

http://cubic.bioc.columbia.edu/eva/

Computer Related > Math and Statistics
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.

NAR Web Server Issue 2003
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tagsautomation protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins reproducibility of results secondary protein structure sequence alignment

GlobPlotTool Content

http://globplot.embl.de/

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

GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.

NAR Web Server Issue 2003
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tagsalgorithms amino acid motifs humans molecular models protein sequence analysis proteome tertiary protein structure

HHrepTool Content

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

Protein > 2-D Structure Prediction
Protein > Sequence Features
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).

NAR Web Server Issue 2006
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tagsamino acid repetitive sequences markov chains protein folding protein sequence analysis sequence alignment

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

NAR Web Server Issue 2003NAR Web Server Issue 2004
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

iPDATool Content

http://biominer.bime.ntu.edu.tw/ipda/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology cluster analysis computational biology computer simulation escherichia coli humans molecular models molecular sequence data protein databases protein sequence analysis proteins secondary protein structure sequence alignment

Tags associated with subcategory 'Protein/2-D Structure Prediction'

secondary protein structure protein sequence analysis proteins algorithms molecular models protein conformation protein databases sequence alignment amino acid sequence computational biology membrane proteins reproducibility of results protein folding tertiary protein structure molecular sequence data humans amino acid sequence homology neural networks (computer) computer simulation statistical models markov chains sensitivity and specificity proprotein convertases cell membrane bacterial genome base sequence anti-infective agents sequence homology archaeal genome automated pattern recognition biomedical engineering chemical dictionaries theoretical models archaeal genes bacterial genes porins bacterial outer membrane proteins computer security database management systems biological models hiv integrase consensus sequence cytochrome p-450 enzyme system discriminant analysis double-blind method escherichia coli software design proteomics rhodopseudomonas protein sorting signals forecasting haemophilus influenzae conserved sequence genetic databases dna tissue plasminogen activator protein structural homology thermodynamics viral genome nucleic acid sequence homology proto-oncogene proteins c-myc sequence analysis chemical models flavodoxin animals factual databases probability amino acids thioredoxins mathematics molecular structure structural models drosophila proteome gene expression x-ray crystallography genome time factors systems integration dna sequence analysis eukaryotic cells evaluation studies as topic genomics histones peptides rna sequence analysis ubiquitin open reading frames salmonella typhimurium initiator codon leghemoglobin gram-negative bacteria cluster analysis binding sites magnetic resonance spectroscopy statistics as topic nucleic acid conformation ligands circular dichroism glycosyltransferases trna methyltransferases