Faster placement of hydrogens in protein structures by dynamic programming

Proceedings of the Sixth Workshop on Algorithm Engineering and Experiments and the First Workshop on Analytic Algorithms and Combinatorics

Volumn , Issue , 2004, Pages 39-48

  Leaver Fay, Andrew ^a   Liu, Yuanxin ^a   Snoeyink, Jack ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOCHEMISTRY; CHEMICAL BONDS; COMPUTER SOFTWARE; DATABASE SYSTEMS; HYDROGEN; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; PROTEINS;

COLLISIONS; DYNAMIC PROGRAMMING ALGORITHMS; ENERGY SCORE FUNCTIONS; PROTEIN DATABANK (PDB);

DYNAMIC PROGRAMMING;

EID: 8344260667     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (6)

1. Hans L. Bodlaender. A tourist guide through treewidth. Technical Report 1992, Dept. Comput. Sci., Utrecht Univ.
2. Simon C. Lovell, Ian W. Davis, W. Bryan Arendall III, Paul I. W. de Bakker, J. Michael Word, Michael G. Prisant, Jane S. Richardson, and David C. Richardson. Structure validation by c-alpha geometry: phi, psi, and c-beta deviation. Proteins: Structure, Function, and Genetics, 50:437-450, 2003.
3. D. C. Richardson and J. S. Richardson. Mage, probe, and kinemages. In M.G. Rossmann and E. Arnold, editors, International Tables for Crystallography, volume F, pages 727-730. Kluwer Publishers, Dordrecht, 2001.
4. J. M. Word, R. C. Bateman Jr., B. K. Presley, S. C. Lovell, and D. C. Richardson. Exploring steric constraints on protein mutations using mage/probe. Protein Sci, 9:2251-2259, 2000.
5. J. Michael Word, Simon C. Lovell, Thomas H. LaBean, Hope C. Taylor, Michael E. Zalis, Brent K. Presley, Jane S. Richardson, and David C. Richardson. Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms. Journal of Molecular Biology, 285:1711-1733, 1999.
6. J. Michael Word, Simon C. Lovell, Jane S. Richardson, and David C. Richardson. Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. Journal of Molecular Biology, 285(4):1735-1747, 1999.