G-contacts: Fast contact search in bio-molecular ensemble data

Computer Physics Communications

Volumn 184, Issue 12, 2013, Pages 2856-2859

  Blau, Christian ^a   Grubmuller, Helmut ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Decomposition scheme; Gromacs; Molecular dynamics; Range search

Indexed keywords

BRUTE-FORCE APPROACH; COMPUTATIONAL BIOPHYSICS; DECOMPOSITION SCHEME; GROMACS; INTERATOMIC INTERACTIONS; RANGE SEARCH; RANGE SEARCH PROBLEMS; STRUCTURAL BIOLOGY;

ALGORITHMS;

MOLECULAR DYNAMICS;

EID: 84888295649     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2013.07.018     Document Type: Article

References (6)

1. M. Zink, and H. Grubmuller Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study Biophysical Journal 96 4 2009 1350 1363
2. J. Klepeis, K.L. Larsen, R. Dror, and D. Shaw Long-timescale molecular dynamics simulations of protein structure and function Current Opinion in Structural Biology 19 2 2009 120 127
3. J. Erickson, and P. Agarwal Geometric range searching and its relatives. advances in discrete and computational geometry Contemporary Mathematics 223 1999 1 56
4. S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M.R. Shirts, J.C. Smith, P.M. Kasson, D.V.D. Spoel, B. Hess, and E. Lindahl Gromacs 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 29 7 2013 845 854
5. D. Knuth The Art of Computer Programming, Vol. 3: Sorting and Searching 1973 Addison-Wesley Reading, MA
6. T. Dieckmann, E. Suzuki, J. Feigon, and G.K. Nakamura Solution structure of an atp-binding rna aptamer reveals a novel fold RNA 2 7 1996 628 640