CAFE

CaFE is a software tool that provides accurate prediction of binding free energy through two popular methods, MM/PBSA and LIE. These methods are commonly used in computational biology and structure-based drug design due to their ability to strike a balance between prediction accuracy and computational efficiency. CaFE is an easy-to-use pipeline tool that leverages the power of VMD and NAMD programs to perform these calculations. It supports multiple static coordinate and molecular dynamics trajectory file formats and various force field parameters, making it versatile and compatible with different molecular simulation packages. The source code and documentation for CaFE are freely available on GitHub under the GNU General Public License, and it is a VMD plugin that can be used on any platform. If you have any questions or need further assistance, please contact the developer at [tingjunhou@zju.edu.cn](mailto:tingjunhou@zju.edu.cn).

Topic

Medicinal chemistry;Molecular dynamics;Immunology

Detail

  • Operation: Phasing;Molecular dynamics;Molecular docking

  • Software interface: Command-line interface

  • Language: -

  • License: The GNU General Public License v3.0

  • Cost: Free with restrictions

  • Version name: -

  • Credit: -

  • Input: -

  • Output: -

  • Contact: Tingjun Hou tingjunhou@zju.edu.cn

  • Collection: -

  • Maturity: Mature

Publications

  • CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
  • Bollen S, et al. CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data. CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data. 2014; 30:1484-5. doi: 10.1093/bioinformatics/btu028
  • https://doi.org/10.1093/bioinformatics/btu028
  • PMID: 24451624
  • PMC: PMC4016701
  • CaFE: a tool for binding affinity prediction using end-point free energy methods.
  • Liu H, et al. CaFE: a tool for binding affinity prediction using end-point free energy methods. Bioinformatics 2016; 32:2216-2218. doi: 10.1093/bioinformatics/btw215
  • https://doi.org/10.1093/bioinformatics/btw215
  • PMID: -
  • PMC: -
  • CAFE: aCcelerated Alignment-FrEe sequence analysis.
  • Lu YY, et al. CAFE: aCcelerated Alignment-FrEe sequence analysis. CAFE: aCcelerated Alignment-FrEe sequence analysis. 2017; 45:W554-W559. doi: 10.1093/nar/gkx351
  • https://doi.org/10.1093/nar/gkx351
  • PMID: 28472388
  • PMC: PMC5793812

Download and documentation

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