About

Learn about our research, publications, and the tools we use to provide accurate predictions.

Citing this web server

Kagami LP, Orlando G, Raimondi D, Ancien F, Dixit B, Gavaldá-García J, Ramasamy P, Roca-Martínez J, Tzavella K, Vranken W. b2bTools: online predictions for protein biophysical features and their conservation. Nucleic Acids Res. 2021 Jul 2;49(W1):W52-W59. doi: 10.1093/nar/gkab425. PMID: 34057475; PMCID: PMC8262692.

Our Predictors

Single Sequence Predictors

DynaMine

Predicts protein backbone dynamics from sequence.

Main publication:

Cilia, E., Pancsa, R., Tompa, P., Lenaerts, T., & Vranken, W. F. (2018). From protein sequence to dynamics and disorder with DynaMine. Nature Communications, 9(1), 1-12.

DisoMine

Predicts protein disorder from sequence.

Main publication:

Cilia, E., Pancsa, R., Tompa, P., Lenaerts, T., & Vranken, W. F. (2018). From protein sequence to dynamics and disorder with DynaMine. Nature Communications, 9(1), 1-12.

EarlyFolding

Predicts early folding residues in proteins.

Main publication:

Cilia, E., Pancsa, R., Tompa, P., Lenaerts, T., & Vranken, W. F. (2018). From protein sequence to dynamics and disorder with DynaMine. Nature Communications, 9(1), 1-12.

AgMata

Predicts aggregation-prone regions in proteins.

Main publication:

Cilia, E., Pancsa, R., Tompa, P., Lenaerts, T., & Vranken, W. F. (2018). From protein sequence to dynamics and disorder with DynaMine. Nature Communications, 9(1), 1-12.

ShiftCrypt

Predicts chemical shifts from protein structures using NMR data.

Main publication:

Cilia, E., Pancsa, R., Tompa, P., Lenaerts, T., & Vranken, W. F. (2018). From protein sequence to dynamics and disorder with DynaMine. Nature Communications, 9(1), 1-12.

Tools and Libraries

Visualization Tools

Bokeh

Bokeh Development Team (2018). Bokeh: Python library for interactive visualization.

MatPlotLib

J. D. Hunter, "Matplotlib: A 2D Graphics Environment," in Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95, May-June 2007.

Mol* Viewer

Sehnal D, et al. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 2021 Jul 2;49(W1):W431-W437.

Structure Prediction Tools

AlphaFold Database

Varadi, M. et al. "AlphaFold Protein Structure Database in 2024: Providing structure coverage for over 214 million protein sequences." Nucleic Acids Research, gkad1011 (2023).

Varadi, M. et al. "AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models." Nucleic Acids Research, 50(D1), pages D439–D444 (2021).

AlphaSync

AlphaSync is an enhanced AlphaFold structure database synchronized with UniProt. Benjamin Lang, M. Madan Babu. bioRxiv 2025.03.12.642845.

Analysis Tools

Clustal Omega

Sievers F, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11;7:539.

Saguaro3D

Segura J, et al. RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies. Bioinformatics. 2022 Jun 13;38(12):3304-3305.

Web Framework

Bootstrap 5

Bootstrap - The most popular HTML, CSS, and JS library in the world.

Django

Django (Version 1.5) [Computer Software]. (2013). Retrieved from https://www.djangoproject.com/.

Attributions

Protein icons created by Freepik - Flaticon
Proteins icons created by Freepik - Flaticon
Magnet icons created by Freepik - Flaticon