Rotamer-dependent Statistical Atomic Potential

• Introduction 

ROTAS is Rotamer-dependent Atomic Statistical potential function derived from known protein structures in the Protein Data Bank for protein structure modeling and quality assessment. The basic building blocks of protein structures are amino acid residues, which have distinguishing physiochemical properties depending on the side-chain conformation. Most of the single covalent bonds in residues allow rotation of the atoms they join, so that the residues have great flexibility. Due to the local steric interactions, residues prefer to adopt only a limited number of staggered conformations, known as rotamers. Depending on the rotameric state, the residue conformation and intra-residue interaction vary significantly, resulting in different solvent accessibility and different electric polarization effect as well as different steric effect on residue atoms. To more accurately describe atomic interactions, ROTAS takes into account the influence of the rotameric state of residues on the specificity of atomic interactions as well as the relative position and orientation of interacting atoms. The performance of ROTAS potential has been tested with various 13 decoy sets, and demonstrated its superiority to other atomic statistical potentials (click here to see the performance comparison).

• Download ROTAS

• Setup and Run

1. Download an executable binary program for your system  

2. Extract the compressed file ("/rotas" directory is automatically created) 

3. Download the energy data file

4. Create an text file and list up the absolute paths of PDB files to be calculated. (one line for each PDB file)

5. Run the ROTAS program with TWO input arguments: the energy data file path and the text file path for pdb list

    For example,

        /rotas/rotas_main /rotas/rotas_energy.mat /rotas/rotas_input.txt

6. Output of ROTAS

1st column : sequence number as listed in the input text file

2nd column : ROTAS energy score 

3rd column :  Distance-dependent energy only

4th column :  Orientation-dependent energy only

• Authors

Jungkap Park(jungkap@umich.edu) and Kazuhiro Saitou(kazu@umich.edu)

Any questions or requests? Please contact to Jungkap Park (jungkap@umich.edu)

• References

Park, J. Saitou, K., 2014, “ROTAS: A Rotamer-dependent, Atomic Statistical Potential for Assessment and Prediction of Protein Structures,” BMC Bioinformatics, 15:307, DOI: 10.1186/1471-2105-15-307