Center for the Study of Systems Biology

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    • Members
  • Skolnick Research Group
    • Jeffrey Skolnick
    • Maximilian Brogi
    • Brendon Cara
    • Chad Choudhry
    • Brice Edelman
    • Jonathan Feldman
    • Jessica Gilmore Forness
    • Bartosz Ilkowski
    • Preetam Jukalkar
    • Giselle McPhilliamy
    • Asha Mira Rao
    • Hargobind Singh
    • Kyle Xu
    • Hongyi Zhou
    • Former Group Members
  • Publications
    • Publications
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  • Software and Services
    • Services
      • DESTINI
      • DR. PRODIS
      • ENTPRISE
      • ENTPRISE-X
      • FINDSITEcomb
      • FINDSITEcomb2.0
      • FRAGSITE
      • FRAGSITE2
      • FRAGSITEcombM
      • Know-GENE
      • LeMeDISCO
      • MEDICASCY
      • MOATAI-VIR
      • PHEVIR
      • PICMOA
    • Downloads
      • AF2Complex
      • AF3Complex
      • APoc
      • Cavitator
      • DBD-Hunter
      • DBD-Threader
      • EFICAz2.5
      • Fr-TM-align
      • GOAP
      • iAlign
      • IS-score
      • LIGSIFT
      • MENDELSEEK
      • PULCHRA
      • SAdLSA
      • Valsci
    • 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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Downloads

 Software (available for download)

  • AF2Complex: Deep-learning based multimeric-protein complex structure prediction
  • APoc: An efficient tool for large-scale structural comparison of protein pockets for interacting with small-molecule ligands.
  • Cavitator: A program for detecting “pocket” or “cavity”, i.e., potential small-molecule binding sites, in a protein structure.
  • DBD-Threader: Identifies DNA-binding domains from a protein’s sequence.
  • DBD-Hunter: Identifies a DNA-binding domain from a protein’s structure.
  • EFICAz2.5: An accurate sequence based approach to enzyme function inference.
  • Fr-TM-align: A program for protein structural alignment that uses the TM-score as the structural comparison metric. This is an improved version of Tm-align.
  • GOAP: A generalized orientation-dependent, all-atom statistical potential for protein structure prediction.
  • iAlign: Structural alignment algorithm for protein-protein interfaces that uses the TM-score as well as a side-chain contact overlap weighted TM-score as the interface comparison metric.
  • IS-score: Is a tool for automatic assessing the quality of protein-protein docking models.
  • LIGSIFT: A new computational method for the structural alignment of small molecules.
  • MENDELSEEK: An algorithm that predicts Mendelian Genes and elucidates what makes them special.
  • PULCHRA: A program for all-atom reconstruction from the backbone C-alpha atoms.
  • SAdLSA: A computational algorithm that performs protein Sequence Alignments from deep-Learning of Structural Alignments.
  • Valsci: An open-source, self-hostable literature review utility for automated large-batch scientific claim verification using LLMs.

Databases

Simulations

Software and Services

  • Skolnick Research Group
    • Jeffrey Skolnick
    • Maximilian Brogi
    • Brendon Cara
    • Chad Choudhry
    • Brice Edelman
    • Jonathan Feldman
    • Jessica Gilmore Forness
    • Bartosz Ilkowski
    • Preetam Jukalkar
    • Giselle McPhilliamy
    • Asha Mira Rao
    • Hargobind Singh
    • Kyle Xu
    • Hongyi Zhou
    • Former Group Members
  • Software and Services
    • Services
      • DESTINI
      • DR. PRODIS
      • ENTPRISE
      • ENTPRISE-X
      • FINDSITEcomb
      • FINDSITEcomb2.0
      • FRAGSITE
      • FRAGSITE2
      • FRAGSITEcombM
      • Know-GENE
      • LeMeDISCO
      • MEDICASCY
      • MOATAI-VIR
      • PHEVIR
      • PICMOA
    • Downloads
      • AF2Complex
      • AF3Complex
      • APoc
      • Cavitator
      • DBD-Hunter
      • DBD-Threader
      • EFICAz2.5
      • Fr-TM-align
      • GOAP
      • iAlign
      • IS-score
      • LIGSIFT
      • MENDELSEEK
      • PULCHRA
      • SAdLSA
      • Valsci
    • Databases
      • Apo and Holo Pairs
      • New Human GPCR Modeling and Virtual Screening
      • PDB-like Structures
    • Simulations
      • E. coli Intracellular Dynamics

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