In-house software and tools

DisoMine

ST resource  DisoMine

Prediction of protein disorder from sequence only

Developers: Gabriele Orlando, Daniele Raimondi,

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

ACPYPE

ST resource  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

ST resource  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

ST resource  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

ST resource  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

ST resource  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

ST resource  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

ST resource  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),

External software and tools from collaborations

RINspector

ST resource  RINspector

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

CING

ST resource  CING

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

SeRenDIP

ST resource  SeRenDIP

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