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 Web search terms

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Chapter 10 Web Search Terms

Using general search terms such as protein structure prediction, or more specific terms such as threading, protein database, amino acid patterns, protein motifs, name of investigator, etc., will usually locate current Web servers for protein analysis and structure prediction. Important Web sites for protein analysis are also discussed throughout this chapter, especially in the tables. There is no chapter table listing Web servers for protein secondary and three-dimensional structure prediction because they are so numerous. Instead, many of these sites are listed below. In most cases, using the search terms in the first column of the table will find the current Web site as the top hit. If the program or server name is not specific enough, then adding additional terms, such as protein structure, should locate the current Web address.

3DPSSM Detection of structural folds by sequence similarity using scoring matrices.
CASP Critical assessment of structure prediction results.
CBS Prediction server Collection of methods for predicting glycosylation and phosphorylation sites and similar tasks.
ChloroP server Prediction of chloroplast transit peptides and cleavage sites.
COILS prediction Prediction of coiled coils by comparison of sequence to a database of coiled-coil proteins.
DAS prediction Prediction of transmembrane helices using dot plots.
DSC structure Discrimination of protein secondary structure class.
EVA evaluation Evaluation site for secondary structure prediction servers.
EXPASY An important resource with many methods for protein analysis, prediction, and modeling.
MTOP Prediction of transmembrane helices and topology.
JPred structure Server for secondary structure prediction in G. J. Barton group; uses set of tools including Jnet with PSI-BLAST search, PHD, DSC, etc.
Libra 1 Resource for threading proteins through structures.
META server Collection of methods for structure prediction including Swiss model, DAS, PHD, PSIPRED, SAM, SSPro, and others.
MODBASE A database of annotated protein structures.
NNPRED Program for secondary structure prediction in the F.E. Cohen laboratory, which also has other programs for structural modeling, loop prediction, etc.
NPSA protein Search for related sequences and performs secondary structure using many different methods (SOPM, SOPMA, HNN, MLRC, DPM, DSC, GOR, PHD, PREDATOR, SIMPA96).
PREDATOR Prediction of secondary structure based on amino acid patterns associated with H bonds.
Predict Protein PHD Predicts secondary structure using neural networks using msa.
PROF Secondary structure prediction by NNs and linear classifiers.
PSA Three-dimensional prediction using HMMs of specific structural classes.
PSI/PRED Secondary structure using NNs and PSI-BLAST position-specific scoring matrices.
PSORT Analyze for protein localization signals.
PSSP Secondary structure prediction by nearest-neighbor method enhanced by msa's.
RADAR Rapid automatic detection and alignment of repeats in protein sequences.
SAM-T02 Structure prediction using HMMs for detecting remote sequence similarity.
Searchlauncher Collection of methods for secondary structure prediction at Baylor College of Medicine.
SignalP server Prediction of signal peptide cleavage sites based on NNs.
Simpa96 Secondary structure prediction by nearest-neighbor method.
SOPM, SOPMA Secondary structure prediction based on sequence similarity.
SPLIT prediction Prediction of membrane protein structure by hydrophobicity scales.
SSP protein Secondary structure prediction by linear discriminant analysis.
SSPro Secondary structure prediction by BRNNs (bidirectional recurrent neural networks).
Swiss-model Structural homology modeling.
TMHMM Prediction of transmembrane helices in proteins using HMMs.
TmPred Prediction of transmembrane regions and their orientation using a database of transmembrane proteins (TMBase).
Touchstone Three-dimensional structure prediction by threading algorithm prospector.
UCLA-DOE server Secondary and three-dimensional structure prediction by sequence similarity and threading using PSI-PRED, SDP (motif-based alignment), and DASEY (directional atomic solvation energy).


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