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RNA prediction

  • RNAcmap: RNA contact map prediction using evolutionary coupling
  • RNAsnap: RNA in vivo Accessible surface area prediction

Protein Structure Prediction

  • SPARKS-X: Fold recognition and template-based structure prediction

Protein Local Structural Prediction

  • SPIDER3: Improved prediction on secondary structure and other structural properties of proteins by LSTM
  • SPIDER2: Predicting secondary structure, local backbone angles, ASA, HSE, and Expected Errors of proteins
  • SPIDER-HSE: Predicting Half-sphere exposure (HSE, alpha and Beta) of proteins
  • SPOT-disorder: Predicting protein disorder by deep bidirectional long short-term memory recurrent neural networks
  • SPOT-disorder2: Predicting protein disorder by an ensemble of deep IncReSenets
  • SPOT-MoRF: Predicting molecular recognition features by transfer learning

Protein Binding site prediction

  • SPRINT: Sequence-based Prediction of protein-peptide binding sites
  • SPRINT-CBH: Sequence-based Prediction of protein-carbohydrate binding sites

Protein Function Prediction

  • SPOT-peptide: Template-based prediction of peptide-binding domains and peptide-binding sites
  • SPOT-ligand: Virtual Drug Screening based on Binding Homology from protein 3D structure
  • SPOT-ligand 2: Virtual Drug Screening based on Binding Homology on expanded template library
  • SPOT-Seq-RNA: RNA Binding Protein Prediction from Sequence
  • SPOT-Struct-RNA: RNA Binding Protein Prediction from 3D structure
  • SPOT-Struct-DNA: DNA Binding Protein Domain Prediction from 3D structure
  • SPOT-CBP: Carbohydrate Binding Protein Domain Prediction

Protein Structure Alignment

  • SPalign: Protein Structure Alignment
  • SPalign-NS: Non-sequential Protein Structure Alignment

Knowledge-based potential function

  • dDFIRE/DFIRE: Monomer Protein Energy Calculation

Gene Variation Analysis

  • DDIG: Detecting Disease-causing Genetic Variations due to Insertion/Deletion and Nonsense mutations
  • EASE-MM: sequence-based prediction of mutation-induced stability changes with feature-based multiple models

Protein Design

  • SPIN: Prediction of the profile of sequences compatible to a protein structure

Other services

  • DDOMAIN: Fast structure-based domain prediction using a normalized domain-domain interaction profile