Secondary Structure Prediction & Assignment

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Analytical Biostatistics Section
[NIH] The ABS offers downloadable software and servers in the areas of sequence analysis, protein structure prediction, ligand binding, and gene expression.

[more info][12372]

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BCM Protein
[Baylor College of Medicine] A secondary structure prediction tool.

[more info][10494]

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BCM Search Launcher: Protein Secondary Structure Prediction
[Baylor College of Medicine] This site allows the selection of any of several secondary structure prediction tools to analyse a protein sequence.

[more info][12261]

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[EMBnet – Swiss Node] “COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.”

[more info][12271]

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Computational Services at EMBL
[EMBL] Ties together sequence search and retrieval, alignment, data submission, comparison and prediction into one site. Also available are tools for structure verification and related software.

[more info][12520]

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EVA: Evaluation of Automatic protein structure prediction
[Columbia University] The EVA service provides a continuous, fully automated, and statistically significant analysis of the accuracy of protein structure prediction servers.

[more info][12411]

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[SBDS] A protein secondary structure predictor.

[more info][10501]

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A Guide to Structure Prediction
[Imperial Cancer Research Fund] A guide with links, giving a generalistic approach to prediction of protein structures.

[more info][10502]

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[EBI] Jnet is a recent neural network protein secondary structure prediction method with an accuracy in the range of 70-76%. It is available for download.

[more info][10525]

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[EBI] “A consensus method for protein secondary structure prediction.”

[more info][12260]

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[Univ. College. London] A multiple sequence prediction program that predicts the secondary structures of multiplicatively aligned sequences using physiochemical information, a set of aligned sequences, and secondary structure decision constants.

[more info][10505]

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Network Protein Sequence @nalysis
[Institute of Biology and Chemistry of Proteins] [email protected] is an interactive Web server dedicated to protein sequence analysis. Analyses offered include sequence similarity, site detection, multiple alignment, secondary structure prediction, and primary structure analysis. Analyses can be combined in a pipeline. The ANTHEPROT windows program is also available here.

[more info][12376]

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[Univ. of California, San Francisco] Predicts the secondary structure of a protein given its sequence.

[more info][10506]

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NNSSP: Nearest-Neighbor Secondary Structure Prediction
[Salamov & Solovyev] Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignment.

[more info][10507]

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[SWBIC] Protein Classification through the Assessment of Predicted Secondary Structure (PCAPSS) is a method for identifying remote protein homologs in the Protein Data Bank that share a similar secondary
structure to the query protein. PCAPSS was designed to be used with orphan or hypothetical proteins, i.e.,
those for which amino acid sequence searches fail to find similar sequences with functional annotation. Its purpose
is to generate hypotheses for structure and function for such hypothetical or putative protein sequences based on
fold recognition.

[more info][10514]

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[University of California, San Francisco] A service for protein secondary structure and class prediction.

[more info][12278]

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[University of Wales, Aberystwyth] This site provides a protein secondary structure prediction system.

[more info][12279]

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[Univ. College London] Analyzes a protein coordinate file and provides details of the structural motifs in the protein.

[more info][11273]

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Protein Secondary Structure Prediction Tools
[ExPASy] An annotated list of links to a number of tools that provide protein secondary structure prediction.

[more info][12268]

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Protein Sequence Analysis
[Sanger Centre] Performs a secondary structure prediction or prosite pattern search.

[more info][10477]

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Protein Structure Prediction Center and CASP
[Lawrence Livermore National Laboratory] “Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. In addition to the support of the CASP meetings our goal is to promote an objective evaluation of prediction methods on a continuing basis.” CASP stands for Critical Assessment of techniques for protein Structure Prediction.

[more info][10441]

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PSA: Protein Sequence Analysis Server
[BMERC] Analyzes amino acid sequences to predict secondary structures and folding classes.

[more info][10513]

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P-SEA Software
[Centre de Biochimie Structurale] This new software assigns secondary structure elements in protein structures from the Ca trace (Labesse G., Colloc’h N., Pothier J. and
Mornon J.-P., CABIOS, vol 13., no. 3, pages 291-295).

[more info][12274]

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[Brunel University] “The PSIPRED protein structure prediction server allows you to submit a protein sequence, perform a prediction of your choice, and receive the results of the prediction via E-mail. You may select one of three prediction methods to apply to your sequence: PSIPRED – a highly accurate secondary structure prediction method, MEMSAT 2 – a new version of our widely used transmembrane topology prediction method, and GenTHREADER – a new sequence profile based fold recognition method.”

[more info][12282]

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Secondary Structure Prediction Methods and Links
[Imperial Cancer Research Fund] A guide on this subject, including descriptions of automaticd methods, manual intervention, strategies, references, and links.

[more info][12283]

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[Pole Bio-Informatique Lyonnais] An improved SOPM method in the prediction of the secondary structure of proteins. Predicts three-state description of the secondary structure (alpha-helix, beta-sheet and coil) of non-homologous proteins.

[more info][10515]

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[UCSC] A hidden Markov Model protein structure prediction server. A library of hidden Markov Models, one per PDB structure and containing approximately 2500 HMMs is on this server.

[more info][10523]