Instruction for the command 'fkcombu' in the "KCOMBU" program

May 12, 2015
Takeshi Kawabata
Laboratory of Protein Informatics
Institute for Protein Research, Osaka University

[Reference for KCOMBU]


The source code of the kcombu is mainly written in C, and developed and executed the linux environment. Some additional programs for 2D graphics and statistical analyses are written in python. For the installation, you need the gcc compiler. If you want to use another compipler, please change the "Makefile" in the "src" directory. The standard installation procedures are as follows:

  1. download the file "kcombu-src-[date].tar.gz" file.
  2. tar zxvf kcombu-src-[date].tar.gz
  3. cd src
  4. make -f Makefile.fkcombu

If the sources is successfully compiled, an execution file "fkcombu" will appear in the "../src" directory.

'fkcombu' : for flexible transforming of a target molecule onto a reference molecule

The program fkcombu flexibly superimpose the target molecule onto the reference molecule. The fkcombu program uses the terms "target" and "reference" in following definitions:

We assume that 3D confomrations of both reference and target molecules are available as the inputs: the 3D conformation of the reference should be experimentally determined, whereas that of target molecule is provided by a conformer generating program. The use of 3D conformation of the receptor protein is optional. 3D structure of the target molecule can be predicted by superimposing and deforming the atoms of target molecule onto that of the tamplate molecule. During the tranforming, bond lengths and bond angles of the target are kept as that of its initial conformation. Therefore, not only a good 3D conformation of the reference, but also a good 3D initial conformation of the target is necessary for the fkcombu program. The program 'fkcombu' mainly uses atomic correspondences obtained by 2D-maximum common substructure (MCS). The target molecule is transformed to superimpose each target atom onto its corresponding reference atom. The details of the calculation of MCS is described in
README_pkcombu.html and README_mcs.html.

Simple Usage

Procedures for transforming

The procedures of program 'fkcombu' consists of following several steps: