molstar

MolStar (MOLecular STructure AnnotatoR)

MolStar is a responsive, easy-to-use JavaScript plugin which enables users to view annotated protein sequence (including variation data from large scale studies) and overlay the annotations over a corresponding experimental or predicted protein structure. It couples protein sequence annotation capabilities provided by ProtVista (or more precisely its modified responsive version implemented when developing MolStar) with structure visualization capabilities provided by LiteMol. Since it does not have any software dependencies and all the data are obtained on the fly, it is easy to integrate it to any web page.

Examples of MolStar's use can be found at https://davidhoksza.github.io/MolStar/ .

The plugin is being developed at the Luxembourg Center for Systems Biomedicine, University of Luxembourg.

Features overview

• Visualization of protein structure as provided by LiteMol
• Annotation of protein sequence as provided by ProtVista
• Mapping of structure on corresponding substring in the sequence
• Automatic retrieval of sequence data based on UniProt ID and corresponding experimental structures from PDB
• Retrieval of predicted models from SWISS-MODEL Repository (SMR) if no PDB structure is available
• Controlling transparency of the structure to see both cartoon and surface view of the structure
• Hovering over position in sequence to highlight it in structure and vice versa
• Color overlay any sequence feature over the structure
• Color overlay all sequence features of given type over the structure
• Color overlay individual variation over the structure
• Color overlay all mutations to given amino acid over the structure
• Color overlay mutation frequency of residues over the structure
• Exports of the structure and annotations to PyMol for advanced inspection

Data sources

• Sequence and annotation data
  • Sequence information comes from UniProt website REST API
  • Sequence annotations are provided by the ProtVista plugin which utilizes the EBI's Proteins REST API. Proteins API includes access to variation, proteomics and antigen services containing "annotations imported and mapped from large scale data sources, such as 1000 Genomes, ExAC (Exome Aggregation Consortium), COSMIC (Catalogue Of Somatic Mutations In Cancer), PeptideAtlas, MaxQB (MaxQuant DataBase), EPD (Encyclopedia of Proteome Dynamics) and HPA, along with UniProtKB annotations for these feature types".
• Structure mapping
  • To obtain the mapping between UniProt and PDB, MolStar is using the SIFTS API, part of the PDBe REST API.
  • In case the SIFTS mapping yields no PDB structures, SMR is queried using its API for available models.
• Structure data
  • In case an experimental structure is available in PDB for given UniProt ID, this structure is downloaded by LiteMol. In this case, MolStar instructs LiteMol to use the mmCIF format.
  • In case there is no experimental structure in PDB, but a model exists in SMR, MolStar instructs LiteMol to use the PDB-format structure data from SMR.

How to use MolStar

• Obtain the JavaScript file with MolStar and link it from your web page
• Create a container DIV (or SPAN) element which will hold the viewer
• Create a JavaScript object and pass it reference to the DIV

The detail description of how to incorporate MolStar into your project can be found in the developer documentation.

Examples of use

Exmpales of how to use MolStar are located in the examples folder.

• See the bare.html file for a bare bones example of how to use the plugin.
• The plugin-page.html is slightly styled plugin usage.
• For an advanced example, see the web directory. It contains a simple web application which enables querying Uniprot (only top 10 matches are retrieved) and for every found record one can click the UniProt ID which creates a new tab with new instance of MolStar for that UniProt ID.

Contributing

We would be happy to hear about your use cases, experiences and ideas/feature requests. Either raise an issue here or get in touch by mail.

Support

Please submit your issues through the MolStar's repository issue tracker available here.

License

This project is licensed under the Apache 2.0 license, quoted below.

Copyright (c) 2018 David Hoksza

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.