Bio2Byte tools web interface

Google Colab integration:

We are pleased to announce that we have recently published a collection of Jupyter Notebooks. These documents provide the opportunity for users to replicate and run the same predictions as found on our website, but utilizing the platform of Google Colab.

The list of notebooks is located at the following link: Bio2Byte public notebooks.

About this page

Our web interface gives integrated access to individual predictors, and includes a novel feature to explore prediction-based 'biophysical variation' of proteins from a multiple sequence alignment (the complete list of the our software tools is available here).

STEP 1: Enter your input sequences

Enter or paste FASTA sequence(s):

Or, upload a new file:
Currently, the system takes FASTA files, a range of multiple sequence alignment (MSA) formats, and the NEF and NMR-STAR formats for NMR chemical shift data (ShiftCrypt).

Original numbering:

N:	CA:	CB:	C:	H:

Select model to use:

Online available tools

Depending on the format of your input data, in the second step of this web interface, you will be able to select predictors from these list:

DynaMine

Prediction of protein backbone dynamics from sequence only
Up to 50 sequences
Min. 5 residues per sequence
Supported format(s): FASTA
Predictions: backbone, sidechain, sheet, helix, coil, polyproline II

EFoldMine

Prediction of protein early folding regions from sequence only
Up to 50 sequences
Min. 5 residues per sequence
Supported format(s): FASTA
Predictions: earlyFolding

DisoMine

Prediction of protein disorder from sequence only
Up to 50 sequences
Min. 5 residues per sequence
Supported format(s): FASTA
Predictions: disoMine

AgMata

Prediction of protein regions that are likely to cause beta-aggregation
Up to 10 sequences
Min. 5 residues per sequence
Supported format(s): FASTA
Predictions: agmata

PSP (Phase Separating Protein)

Predict whether a protein is likely to phase-separate with a particular mechanism involving RNA interacts (FUS-like proteins)
Up to 20 sequences
Min. 20, max. 3000 residues per sequence
Supported format(s): FASTA
Predictions: PSPer score, Complexity, Tyr, Arg, RRM, Disorder

ShiftCrypt

Enable the compression of chemical shift information for proteins into single per-residue values that reflect the in-solution biophysical properties of those residues
Up to 50 sequences
Min. 5 residues per sequence
Supported format(s): NEF, NMR-Star
Predictions: ShiftCrypt score

MSA Tools

Prediction of biophysical parameters (from DynaMine, DisoMine, and EFoldMine) within the multiple sequence alignment (MSA).
Up to 200 aligned sequences
Min. 5 residues per sequence
Supported format(s): CLUSTAL, FASTA, BaliBase, PSI, A3M, Blast, PHYLIP, STOCKHOLM
Predictions: backbone, sidechain, sheet, helix, coil, polyproline II, earlyFolding, disoMine

Alternative methods

This tools are also available directly through an REST API, find the guidelines and examples on the API documentation section. In addition, we provide a Python Package with all our tools (Single Sequence, MSA, and general tools such as parsing and plotting) to enable you to integrate these predictors in your pipelines. For more information, please visit our site on the Python Package Index: b2BTools package.

Further information

Please read the usage guidelines provided on the tutorial section. If you have any feedback or found an issue, please contact us using the feedback from. Read our Terms of use if you are concerned with your privacy and how we handle personal information.