Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling.

@article{Li2006AssignmentOP,
  title={Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling.},
  author={Xin Li and Matthew P. Jacobson and Kai Zhu and Suwen Zhao and Richard A. Friesner},
  journal={Proteins},
  year={2006},
  volume={66 4},
  pages={
          824-37
        }
}
We have developed a new method (Independent Cluster Decomposition Algorithm, ICDA) for creating all-atom models of proteins given the heavy-atom coordinates, provided by X-ray crystallography, and the pH. In our method the ionization states of titratable residues, the crystallographic mis-assignment of amide orientations in Asn/Gln, and the orientations of OH/SH groups are addressed under the unified framework of polar states assignment. To address the large number of combinatorial… CONTINUE READING

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