The node develops and maintains a wide catalogue of predictive bioinformatics web servers and databases, originally
published at biocomp.unibo.it/predictors.html
and biofold.org/resources.html. A growing
subset is formally registered in the bio.tools registry
(marked bio.tools) as part of the node's contribution to the ELIXIR Tools Platform.
Variant effect & disease-gene prediction
| Resource | Description |
|---|
| PhD-SNP bio.tools | SVM-based predictor of disease-associated vs. neutral human single-nucleotide variants. |
| PhD-SNPg bio.tools | Genome-wide variant pathogenicity predictor covering coding and non-coding positions. |
| SNPs&GO bio.tools | Combines sequence, profile and Gene Ontology features to classify disease variants. |
| WS-SNPs&GO | Web-service version of SNPs&GO for high-throughput variant annotation (unconfirmed in bio.tools). |
| E-SNPs&GO | Embedding-based evolution of SNPs&GO using protein language-model features. |
| Meta-SNP bio.tools | Consensus meta-predictor combining multiple variant-effect scores. |
| INPS-MD bio.tools | Predicts the impact of single point variants on protein stability (ddG). |
| DDGun | Sequence-based predictor of protein stability change upon mutation (unconfirmed in bio.tools). |
| DDGemb bio.tools | Structure/sequence-based predictor of protein stability change upon mutation. |
| I-Mutant (1.0/2.0/3.0 Suite) | Classic SVM tool estimating stability change of point mutations from sequence or structure. |
| DrCancer | Predicts cancer driver vs. passenger missense variants. |
| Fido-SNP | Predictor of pathogenic variants trained on functional-impact features. |
| ContrastRank | Ranks candidate disease variants by contrastive scoring of functional annotations. |
| PhenPath | Links human gene variants to phenotype/pathway associations. |
Protein structure, stability & folding
| Resource | Description |
|---|
| K-Fold / K-Pro | Structural/energetic analysis tools supporting protein-folding studies. |
| ThermoScan | Scans sequences/structures for thermostability-related features. |
| SARA / SARA-Coffee | Structural alignment of RNA 3-D structures and sequence-structure alignment of RNA. |
| WebRASP | Web server for RNA/protein statistical potential-based structural scoring. |
| FT-COMAR | Reconstructs 3-D protein models from predicted contact/distance maps. |
| CORNET | Neural-network predictor of residue contact maps. |
| Alpha&ESM hFolds | Repository/analysis portal for AlphaFold and ESMFold human protein models. |
| PONGO | Resource for exploring and comparing predicted protein structural models. |
Membrane proteins & subcellular localisation
| Resource | Description |
|---|
| BUSCA bio.tools | Integrated prediction of sub-cellular localization, signal/transit peptides, GPI-anchors and membrane topology. |
| DeepSig bio.tools | Deep-learning discrimination of signal peptides from transmembrane regions and other N-termini. |
| CoCoNat bio.tools | Coiled-coil domain prediction and oligomerization-state classification. |
| BetAware / BetAware-Deep bio.tools | Predicts topology of outer-membrane beta-barrel proteins. |
| DeepMito bio.tools | Predicts sub-mitochondrial localization of proteins. |
| MemLoci | Predicts sub-cellular localization of membrane proteins (unconfirmed in bio.tools). |
| MemPype bio.tools | Predicts sub-cellular localization of membrane proteins. |
| DisLocate bio.tools | Detects dual sub-cellular localization from sequence. |
| PredGPI bio.tools | Predicts GPI-anchor attachment sites and omega-sites. |
| SChloro | Predicts sub-chloroplast localization of plant proteins. |
| SVMyr | Predicts N-terminal myristoylation sites. |
| TPpred / TPpred2 / TPpred3 | Predicts organelle targeting peptides (mitochondrial/chloroplast transit peptides). |
| DeepREx | Predicts residue-level solvent exposure/relative accessibility. |
| E-pRSA | Embedding-based predictor of relative solvent accessibility. |
| DeepSig bio.tools | Deep-learning discrimination of signal peptides from transmembrane regions and other N-termini. |
| SPEPLip | Signal-peptide and lipoprotein signal cleavage-site prediction (unconfirmed in bio.tools). |
Protein-protein interaction & function
| Resource | Description |
|---|
| ISPRED4 / ISPRED-SEQ | Predicts protein-protein interaction sites from structure or sequence. |
| HIPPIE | Predicts protein interaction partners/hotspots. |
| NET-GE / NETGE-PLUS | Functional enrichment analysis of gene/protein networks. |
| BAR / BAR+ / BAR 3.0 | Bologna Annotation Resource: automated functional annotation (GO terms) of protein sequences. |
| eDGAR | Database of Disease-Gene Associations with Regulatory information. |
| eSLDB | Eukaryotic Subcellular Localization Database integrating predictions and annotations. |
| BENZ WS | Automatic EC-number annotation of enzymes from sequence. |
| DBMFHS | Database of membrane and folding/structure-related lipid data. |
| TRAMPLE / ZenPatches | Analysis of protein surface patches and interaction-prone regions. |
| YAP | Sequence-structure alignment utility. |
| Bioinformatic Sweeties | Educational/outreach bioinformatics web resource. |
