DynaMine
Prediction of protein backbone dynamics from sequence only
Developers: Elisa Cilia, Tom Lenaerts, Rita Pancsa,
Funding: BB2B 2010-1-12 (Innoviris),
Bio2Byte tools
The software tools you can use for your research.
In-house software and tools
For most of below tools, we now have the b2bTools one-stop file upload location where you can easily try them.
EFoldMine
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),
DisoMine
Prediction of protein disorder from sequence only
Developers: Gabriele Orlando, Daniele Raimondi,
Funding: G.0328.16N (FWO), Ph.D. grant Daniele Raimondi (IWT),
DEOGEN2
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),
ACPYPE
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.
PhyloCys
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
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
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
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
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
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),
b2bTools
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, Bhawna Dixit, Jose Gavaldá-García, Luciano Kagami, Gabriele Orlando, Daniele Raimondi, Pathmanaban Ramasamy, Joel Roca Martinez, Konstantina Tzavella, Wim Vranken,
Funding: G.0328.16N (FWO), RNAct (EC),
External software and tools from collaborations
RINspector
RINspector is a CytoScape app that combines protein-structure based network analysis with DynaMine predictions
CING
CING is a software suite for the validation of NMR structure ensembles.
SeRenDIP
Sequence-based Homo- and Heteromeric Protein-protein Interaction sites prediction using Random Forest; a key feature of this method are the DynaMine predictions