Skip to main content

Descriptors for Protein Sequences?


Does anyone know of a website/web service that calculates a series of descriptors of a protein sequence, analogous to the descriptors that are regularly calculated for small molecules.

Specifically what I'm looking for is something that gives a large set of descriptors for either a sequence, or for a given stable identifier (e.g. UniProt ID). The descriptors I'd like back would be things like Molecular weight, number of each amino acid, fraction of each amino acid, hydrophobicity values, complexity/sequence entropy values, number of transmembrane helices, presence of certain features (e.g. signal sequence, nuclear localisation sequence, etc.), domain counts would be good as well - building up a 'fingerprint' for the sequence. I guess with a little bit of thought, it would be possible to come up with a fuller list of descriptors, and the above certainly isn't exclusive, but you get the idea; I'm sure. To be clear, I don't want an annotation service, I just want some numerical/logical feature descriptors.

Does something like this exist, should it be built if not, and so forth?

Comments

Di and tripeptides generated from sequence are the most simple one, and I think you don't need a web serive for that. It's quit easy to implement.
jpo said…
You're right, for small peptides it is quite straightforward to enumerate, and then calculate classical small molecule type features, but what I am after is a set of descriptors for arbitrary length sequences, and that have more 'biological context' - a sort of 'functional group' sort of analogue.
John, the CDK has some protein descriptors, and MW can be done too, and AA count is not there but trivial. What is the input? The sequence, a PDB id or a PDB file?
Matteo Floris said…
Pepstats is a command line tool from the EMBOSS suite which is a source of descriptors: http://emboss.sourceforge.net/apps/cvs/emboss/apps/pepstats.html
Unknown said…
You could try our R package protr: http://cran.r-project.org/web/packages/protr/ or the web app ProtrWeb: http://cbdd.csu.edu.cn:8080/protrweb/ . They provide several state-of-the-art protein sequence-derived structural and physicochemical descriptors. : )

Popular posts from this blog

ChEMBL 34 is out!

We are delighted to announce the release of ChEMBL 34, which includes a full update to drug and clinical candidate drug data. This version of the database, prepared on 28/03/2024 contains:         2,431,025 compounds (of which 2,409,270 have mol files)         3,106,257 compound records (non-unique compounds)         20,772,701 activities         1,644,390 assays         15,598 targets         89,892 documents Data can be downloaded from the ChEMBL FTP site:  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/ Please see ChEMBL_34 release notes for full details of all changes in this release:  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/chembl_34_release_notes.txt New Data Sources European Medicines Agency (src_id = 66): European Medicines Agency's data correspond to EMA drugs prior to 20 January 2023 (excluding vaccines). 71 out of the 882 newly added EMA drugs are only authorised by EMA, rather than from other regulatory bodies e.g.

New SureChEMBL announcement

(Generated with DALL-E 3 ∙ 30 October 2023 at 1:48 pm) We have some very exciting news to report: the new SureChEMBL is now available! Hooray! What is SureChEMBL, you may ask. Good question! In our portfolio of chemical biology services, alongside our established database of bioactivity data for drug-like molecules ChEMBL , our dictionary of annotated small molecule entities ChEBI , and our compound cross-referencing system UniChem , we also deliver a database of annotated patents! Almost 10 years ago , EMBL-EBI acquired the SureChem system of chemically annotated patents and made this freely accessible in the public domain as SureChEMBL. Since then, our team has continued to maintain and deliver SureChEMBL. However, this has become increasingly challenging due to the complexities of the underlying codebase. We were awarded a Wellcome Trust grant in 2021 to completely overhaul SureChEMBL, with a new UI, backend infrastructure, and new f

Accessing SureChEMBL data in bulk

It is the peak of the summer (at least in this hemisphere) and many of our readers/users will be on holiday, perhaps on an island enjoying the sea. Luckily, for the rest of us there is still the 'sea' of SureChEMBL data that awaits to be enjoyed and explored for hidden 'treasures' (let me know if I pushed this analogy too far). See here and  here for a reminder of SureChEMBL is and what it does.  This wealth of (big) data can be accessed via the SureChEMBL interface , where users can submit quite sophisticated and granular queries by combining: i) Lucene fields against full-text and bibliographic metadata and ii) advanced structure query features against the annotated compound corpus. Examples of such queries will be the topic of a future post. Once the search results are back, users can browse through and export the chemistry from the patent(s) of interest. In addition to this functionality, we've been receiving user requests for  local (behind the