Center for the Study of Systems Biology

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  • Skolnick Research Group
    • Jeffrey Skolnick
    • Courtney Astore
    • Hongnan “Conan” Cao
    • Mu Gao
    • Jessica Gilmore Forness
    • Bartosz Ilkowski
    • Hongyi Zhou
    • Former Group Members
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  • Software and Services
    • Services
      • DESTINI
      • DR. PRODIS
      • ENTPRISE
      • ENTPRISE-X
      • FINDSITEcomb
      • FINDSITEcomb2.0
      • Know-GENE
      • MEDICASCY
    • Downloads
      • APoc
      • Cavitator
      • DBD-Hunter
      • DBD-Threader
      • EFICAz2.5
      • Fr-TM-align
      • GOAP
      • iAlign
      • IS-score
      • LIGSIFT
      • PULCHRA
      • SAdLSA
    • Databases
      • Apo and Holo Pairs
      • New Human GPCR Modeling and Virtual Screening
      • PDB-like Structures
    • Simulations
      • E. coli Intracellular Dynamics
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    • ARCHIVE: Distinguished Lecture Series in Systems Biology
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Software and Services

Online Services

Ligand Docking/Screening
  • FINDSITEcomb: A tool for large scale virtual ligand screening. It offers the advantage that comparable results are obtained when predicted or experimental structures are used. The user can either provide a protein structure in PDB format or a protein sequence whose structure will first be predicted prior to its use in virtual ligand screening.
  • FINDSITEcomb2.0: An upgrade of the FINDSITEcomb algorithm that was compared to several commercially and freely available docking programs against the DUD set.
Personalized Medicine
  • ENTPRISE: An algorithm for predicting human disease-associated amino acid mutations from sequence entropy and predicted protein structures.
  • ENTPRISE-X: An algorithm for predicting human disease-associated frameshift & nonsense mutations.
  • DR. PRODIS: A comprehensive prediction of drug-protein interactions, side effects, toxicity and disease associations for the human proteome.
  • Know-GENE: A knowledge-based approach to predict gene–disease associations.
  • MEDICASCY: A multi-label based boosted random forest machine learning method that predicts small molecule’s side effects, indications, efficacy and mode of action proteins.
Protein Structure Prediction
  • DESTINI: A deep-learning based contact-driven protein structure prediction tool.

Downloads

Databases

Simulations

  • Skolnick Research Group
    • Jeffrey Skolnick
    • Courtney Astore
    • Hongnan “Conan” Cao
    • Mu Gao
    • Jessica Gilmore Forness
    • Bartosz Ilkowski
    • Hongyi Zhou
    • Former Group Members
  • Software and Services
    • Services
      • DESTINI
      • DR. PRODIS
      • ENTPRISE
      • ENTPRISE-X
      • FINDSITEcomb
      • FINDSITEcomb2.0
      • Know-GENE
      • MEDICASCY
    • Downloads
      • APoc
      • Cavitator
      • DBD-Hunter
      • DBD-Threader
      • EFICAz2.5
      • Fr-TM-align
      • GOAP
      • iAlign
      • IS-score
      • LIGSIFT
      • PULCHRA
      • SAdLSA
    • Databases
      • Apo and Holo Pairs
      • New Human GPCR Modeling and Virtual Screening
      • PDB-like Structures
    • Simulations
      • E. coli Intracellular Dynamics

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