What is ToMoCoMD-CAMP MuLiMs?

The MuLiMs’ programs (v1.0) allow easy calculation of algebraic forms-based molecular descriptors. Here, three modules are included, a) MuLiMs-GCoMPAs, b) MuLiMs-MCoMPAs and c) MuLiMs-SCoMPAs. They are based on the application of mathematical n-linear transformations using 2-4 n-tuple matrix representations. This version has some relevant features, such as:

  • One chemical input format (PDB files)
  • A sub module for the preparation of biomacromolecular datasets to perform calculations (removing hydrogen and HET atoms). This module also allows the selection of the model in the case of Nuclear Magnetic Resonance (NMR) experimental data and the chain (s) of interest to the investigator.
  • The generation of seven 3D-protein representations by filtering the atomic spatial coordinates (x,y,z) of : Alpha-Carbon, Beta-Carbon, Amide-Bond Carbon, Alpha and Beta Carbons, Side-Chain Atoms and All atoms to perform descriptors calculations
  • Sixteen properties as amino acid weightings: Side-chain Mass, Side-chain Volume, Z1-scale and son on.
  • Ten properties as atom weightings: Electronegativity, Mass, Radii and so on.
  • Three matrix representations: non-, simple-stochastic and mutual probabilistic.
  • One new matrix form by using cutoffs (lag k/r)
  • Thirty local indices classified into in three categories: Amino-Acid type: Apolar, Polar positively charged, Polar negatively charged and so on, Secondary Structure Preference: Alpha helix favoring Amino-Acids, Beta-Sheets favoring Amino-Acids and so on and R group (one for each α-aminoacid) including Alanine, Arginine and so on.
  • Three output file formats, Space Delimited Text file, Weka ARFF file and Comma Separated Values file.
  • The distance to the protein molecule center could be into consideration as diagonal entries
  • Several invariants that generalize the initial form of obtaining indices from amino acidic (or fragment) contributions; the new indices are obtained by using these invariants on LAIs (Local Amino Acidic Invariants) vector that include amino acidic indices
  • Calculations with enhanced speed by using of all CPU cores