Here is a collection of online/web services I've developed as part of my work at Ensembl or while doing research on Machine Learning applied to protein structure prediction problems.
A centralised repository for registering and discovering publicly accessible track hubs, to allow third parties willing to share their data to advertise their services, and to make it easier for researchers around the workd to discover and use hubs containing different types of genomic research data. The Registry provides an intuitive and easy to use search interface, and RESTful APIs for registering and searching track hubs, checking if a track hub is still available and obtain information which can be used by genome browsers to build convenient interfaces.
A Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. It also provides bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language.
DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. Optionally, disulfide connectivity can be predicted from sequence and a bonding state assignment given as input. The output is a simple visualization of the assigned bonding state (with confidence degrees) and the most likely connectivity patterns.
Distill is a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of Cα traces for short proteins (up to 200 amino acids).
CSpritz is a web server for the prediction of intrinsic protein disorder. The server provides a global output page, for download and simultaneous statistics of all predictions. Links are provided to each individual protein where the amino acid sequence and disorder prediction are displayed along with statistics for the individual protein. As a novel feature, CSpritz provides information about structural homologues as well as secondary structure and short functional linear motifs in each disordered segment.