meta-PPISP: a meta web server for protein-protein interaction site prediction

A number of complementary methods have been developed for predicting protein-protein interaction sites. We sought to increase prediction robustness and accuracy by combining results from different predictors, and report here a meta web server, meta-PPISP, that is built on three individual web servers: cons-PPISP (http://pipe.scs.fsu.edu/ppisp.html), Promate (http://bioportal.weizmann.ac.il/promate), and PINUP (http://sparks.informatics.iupui.edu/PINUP/). A linear regression method, using the raw scores of the three servers as input, was trained on a set of 35 nonhomologous proteins. Cross validation showed that meta-PPISP outperforms all the three individual servers. At coverages identical to those of the individual methods, the accuracy of meta-PPISP is higher by 4.8 to 18.2 percentage points. Similar improvements in accuracy are also seen on CAPRI and other targets. AVAILABILITY: meta-PPISP can be accessed at http://pipe.scs.fsu.edu/meta-ppisp.html     

MHCPred: A server for quantitative prediction of peptide-MHC binding

Accurate T-cell epitope prediction is a principal objective of computational vaccinology. As a service to the immunology and vaccinology communities at large, we have implemented, as a server on the World Wide Web, a partial least squares-based multivariate statistical approach to the quantitative prediction of peptide binding to major histocom- patibility complexes (MHC), the key checkpoint on the antigen presentation pathway within adaptive cellular immunity. MHCPred implements robust statistical models for both Class I alleles (HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203, HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3301, HLA-A*6801, HLA-A*6802 and HLA-B*3501) and Class II alleles (HLA-DRB*0401, HLA-DRB*0401 and HLA-DRB*0701). MHCPred is available from the URL: http://www.jenner.ac.uk/MHCPred.     

Mfold web server for nucleic acid folding and hybridization prediction

The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.     

T-Epitope Designer: A HLA-peptide binding prediction server

The current challenge in synthetic vaccine design is the development of a methodology to identify and test short antigen peptides as potential T-cell epitopes. Recently, we described a HLA-peptide binding model (using structural properties) capable of predicting peptides binding to any HLA allele. Consequently, we have developed a web server named T-EPITOPE DESIGNER to facilitate HLA-peptide binding prediction. The prediction server is based on a model that defines peptide binding pockets using information gleaned from X-ray crystal structures of HLA-peptide complexes, followed by the estimation of peptide binding to binding pockets. Thus, the prediction server enables the calculation of peptide binding to HLA alleles. This model is superior to many existing methods because of its potential application to any given HLA allele whose sequence is clearly defined. The web server finds potential application in T cell epitope vaccine design. AVAILABILITY: http://www.bioinformation.net/ted/     

XtalPred: a web server for prediction of protein crystallizability

XtalPred is a web server for prediction of protein crystallizability. The prediction is made by comparing several features of the protein with distributions of these features in TargetDB and combining the results into an overall probability of crystallization. XtalPred provides: (1) a detailed comparison of the protein's features to the corresponding distribution from TargetDB; (2) a summary of protein features and predictions that indicate problems that are likely to be encountered during protein crystallization; (3) prediction of ligands; and (4) (optional) lists of close homologs from complete microbial genomes that are more likely to crystallize. AVAILABILITY: The XtalPred web server is freely available for academic users on http://ffas.burnham.org/XtalPred     

ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors

ClusterDraw is a program aimed to identification of binding sites and binding-site clusters. Major difference of the ClusterDraw from existing tools is its ability to scan a wide range of parameter values and weigh statistical significance of all possible clusters, smaller than a selected size. The program produces graphs along with decorated FASTA files. ClusterDraw web server is available at the following URL: http://flydev.berkeley.edu/cgi-bin/cld/submit.cgi