Center for the Study of Systems Biology

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EFICAz2.5

EFICAz2.5 (Enzyme Function Inference by a Combined Approach) is an automatic engine for large-scale enzyme function inference that combines predictions from six different methods developed and optimized to achieve high prediction accuracy: (i) recognition of functionally discriminating residues (FDRs) in enzyme families obtained by a Conservation-controlled HMM Iterative procedure for Enzyme Family classification (CHIEFc), (ii) pairwise sequence comparison using a family specific Sequence Identity Threshold, (iii) recognition of FDRs in Multiple Pfam enzyme families, (iv) recognition of multiple Prosite patterns of high specificity, (v) SVM evaluation of CHIEFc families, and (vi) SVM evaluation of Multiple Pfam enzyme families.

If you find use EFICAz2.5 useful, please cite the following papers:

  • Narendra Kumar and Jeffrey Skolnick (2012) EFICAz2.5: Application of a high-precision enzyme function predictor to 396 proteomes. Bioinformatics 28(20):2687-2688. PDF
  • Arakaki A, Huang Y and Skolnick J (2009) EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. BMC Bioinformatics 10:107 PDF
  • Tian W, Arakaki AK, Skolnick J (2004) EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic Acids Research 32(21):6226-39. PDF

This software is freely available to ALL users.

Download EFICAz

latest
release 1.3

Instructions for installation and usage of EFICAz2.5 are included in the package. To run EFICAz2 (release 1.3), use the following command:
$> python $EFICAZ_PATH/EFICAz_latest.py input_sequence_fasta

  • 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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