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.

Found 77 links

Displaying 15 links

Align-GVGDTool Content

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Align-GVGD is a freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. Align-GVGD is an extension of the original Grantham difference to multiple sequence alignments and true simultaneous multiple comparisons.

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AlignMeTool Content

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AlignMe (for Alignment of Membrane Proteins) can be used to examine detailed similarity between homologous proteins even if there is no notable sequence similarity. The predefined gap/weight sets have been optimized for membrane proteins, and so should be particularly useful for these difficult cases.

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AlphaPredTool Content

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The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.

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BetaTPredTool Content

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The server BetaTPred is developed for predicting ß-turns in a protein from the amino acid sequence. It allows the user * to predict turns in a protein using existing statistical algorithms. * to predict the type of ß-turn such as Type I, I', II, II', VI, VIII and non-specific i.e., advanced prediction. * to predict the consensus ß-turn in a protein.

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BetatPred2Tool Content

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The aim of BetaTPred2 server is to predict ß turns in proteins from multiple alignment by using neural network from the given amino acid sequence. For ß turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED.

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BetaturnsTool Content

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The aim of Betaturns server is to predict different types of turns such as Types I, II, IV, VIII and non-specific in a given amino acid sequence. The method is based on neural network.

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Bioinformatics ToolkitTool Content

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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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BOMPTool Content

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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.

BPROMPTTool Content

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Bayesian PRediction Of Membrane Protein Topology (BPROMPT) uses a Bayesian Belief Network to combine the results of other membrane protein prediction methods for a protein sequence.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
BPROMPT: A consensus server for membrane protein prediction200337

COILSTool Content

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Prediction of coiled coil regions.

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links directory index: 2781
TitlePublication YearGoogle Scholar Citation Count
Predicting coiled coils from protein sequences19912781

DICHROWEBTool Content

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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.

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