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. |
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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). |