About CMASA_flex

CMASA_flex package is a powerful software for detecting local structural similarity from whole structures with the sequence independent. It can search more than 30 and unconserved residues (eg. ligand binding sites) to a large database such as nrPDB, nrSCOP. Thus, it can be applied to different fields: predicting ligand binding sites, predicting protein-ligand interactions, detecting remote homologous, detecting convergent cases, protein functional annotation, drug design and other fields that need to detect local structural similarity.

CMASA_flex package can not only be used when a structured protein search to a functional site database (eg., ligand-binding sites, CSA, et,al), but also can be used as a local structure search to a large database(e.g., nrSCOP, nrPDB). You can create own defined database by makeCMASAdb included in this package.

Note: CMASA_flex is now just a beta version; we will update it immediately after the official version was completed.


Web server:

Paste a structure:

Or upload a structure:

Select a database:

Request a jobID:


CMASA_flex is written by C/C++, and under GPL(GNU Lesser General Public License) license. It can be freely downloaded.

Download CMASA_flex files: CMASA_flex

CMASA_flex contains: binary files, source code files, searchable data files, and predicted db files.

Only binary files are required for CMASA_flex.

If you want to run CMASA_flex in linux, especailly run it in the supermachine, you may compile the CMASA_flex from the source code files.

We recommand that you download all the searchable data files.

If you are interested in what we have done, or you need our predictions to further analysis, you can download the predicted db files.


please e-mail to: ligonghua@mail.kiz.ac.cn or ligonghua_88@yaoo.com.cn