Bio2Byte tools

Prediction of protein backbone dynamics from sequence only

Developers: Elisa Cilia, Tom Lenaerts, Rita Pancsa,

Funding: BB2B 2010-1-12 (Innoviris),

Prediction of protein early folding regions from sequence only

Developers: Taushif Khan, Gabriele Orlando, Daniele Raimondi,

Funding: G.0328.16N (FWO), Ph.D. grant Daniele Raimondi (IWT),

Prediction of protein disorder from sequence only

Developers: Gabriele Orlando, Daniele Raimondi,

Funding: G.0328.16N (FWO), Ph.D. grant Daniele Raimondi (IWT),

Predicting the effect of amino acid mutations in human proteins

Developers: Tom Lenaerts, Daniele Raimondi, Marianne Rooman,

Funding: Ph.D. grant Daniele Raimondi (IWT), ICITY-RDI.BRU (ICITY),

PhyloCys is a tool to predict cysteine disulphide bonding patterns in proteins from evolutionary sequence information.

Developers: Gabriele Orlando, Daniele Raimondi,

Funding: BB2B 2010-1-12 (Innoviris), Ph.D. grant Daniele Raimondi (IWT),

Sephiroth is a tool to predict the cysteine disulphide bonding pattern in proteins from evolutionary sequence information.

Developers: Gabriele Orlando, Daniele Raimondi,

Funding: BB2B 2010-1-12 (Innoviris), Ph.D. grant Daniele Raimondi (IWT),

Rigapollo is an SVM-dependent pairwise HMM tool for protein pairwise alignments.

Developers: Gabriele Orlando, Daniele Raimondi,

Funding: G.0328.16N (FWO), Ph.D. grant Daniele Raimondi (IWT),

Agmata is a single-sequence based predictor of protein regions that are likely to cause beta-aggregation. It is based on a model that uses the biophysical predictions of protein behaviour, not on amino acid codes directly.

Developers: Gabriele Orlando, Daniele Raimondi,

Funding: G.0328.16N (FWO),

ShiftCrypt enables the compression of chemical shift information for proteins into single per-residue values that reflect the in-solution biophysical properties of those residues. You can also align proteins based on the ShiftCrypt value.,

Developers: Luciano Kagami, Gabriele Orlando, Daniele Raimondi,

Funding: G.0328.16N (FWO),

PSP (Phase Separating Protein) enables you to predict whether a protein is likely to phase-separate with a particular mechanism involving RNA interacts (FUS-like proteins). It will highlight the regions in your protein that are involved mechanistically, and provide an overall score.

Developers: Gabriele Orlando, Daniele Raimondi,

Funding: G.0328.16N (FWO), Ph.D. grant Daniele Raimondi (IWT),

Our new b2bTools 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.

Developers: François Ancien, David Bickel, Danh Bui-Thi, Charlotte Crauwels, Adrian Diaz, Bhawna Dixit, Jose Gavaldá-García, Sophie-Luise Heidig, Luciano Kagami, Gabriele Orlando, Daniele Raimondi, Pathmanaban Ramasamy, Joel Roca Martinez, Konstantina Tzavella, Wim Vranken,

Funding: G.0328.16N (FWO), RNAct (EC),

ACPYPE enables the generation of topology files for molecular dynamics simulations. It will be moved from its current location to the internal resources during late 2018/early 2019.

Developers: Luciano Kagami, Wim Vranken,

Funding: No funding associated.

https://doi.org/10.1093/bioinformatics/btad350

With RRMScorer you can predict which RNA triplet a given RNA recognition motif (RRM) domain is likely to bind. The website visualises the results and gives extensive additional information about the prediction. Note that the RRMScorer predictions are restricted to the 'canonical' RNA binding mode of RRMs. More information: https://doi.org/10.1093/nar/gkaf367

Developers: Adrian Diaz, Joel Roca Martinez,

Funding: RNAct (EC),

https://doi.org/10.1371/journal.pcbi.1010859

https://doi.org/10.1093/nar/gkaf367

ConStaVa is a tool for the probabilistic interpretation of large conformational ensembles (e.g. from MD simulations or for intrinsically disordered proteins). Through analysis of phi/psi angle distributions, it detects six conformational states and calculates the associated 'conformational state variability'. It so moves away from traditional fixed secondary structure interpretation of models to a more ensemble-oriented interpretation that is useful for dynamic regions of proteins.

Developers: David Bickel, Adrian Diaz, Jose Gavaldá-García, Wim Vranken,

Funding: RNAct (EC), ProteinContour (FWO),

https://doi.org/10.1093/nargab/lqae082

https://github.com/bio2byte/constava

SIMSApiper is a Nextflow pipeline that enables users to create structure informed multiple sequence alignments simply from a set of protein sequences. Structural information may be provided by the user or directly retrieved by the pipeline (AlphaFold Database or ESMFold). The process is significantly sped up by using sequence identity-based subsets and aligning them in parallel. Conserved secondary structure elements are used to reduce gaps for a high-quality final alignment.

Developers: Charlotte Crauwels, Adrian Diaz, Sophie-Luise Heidig,

Funding: PhD grant (FNRS),

https://doi.org/10.1093/bioinformatics/btae276

RINspector is a CytoScape app that combines protein-structure based network analysis with DynaMine predictions

CING is a software suite for the validation of NMR structure ensembles.

Sequence-based Homo- and Heteromeric Protein-protein Interaction sites prediction using Random Forest; a key feature of this method are the DynaMine predictions