FRAGSION: Ultra-fast protein fragment library generation by IOHMM sampling

Bioinformatics

Volumn 32, Issue 13, 2016, Pages 2059-2061

  Bhattacharya, Debswapna ^a   Adhikari, Badri ^a   Li, Jilong ^a   Cheng, Jianlin ^a,b  

^a University of Missouri   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE LIBRARY; PROTEIN;

AMINO ACID SEQUENCE; CHEMISTRY; MARKOV CHAIN; PEPTIDE LIBRARY; PROTEIN SECONDARY STRUCTURE; SOFTWARE;

AMINO ACID SEQUENCE; MARKOV CHAINS; PEPTIDE LIBRARY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOFTWARE;

EID: 85007170449     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw067     Document Type: Article

References (12)

1. Berman,H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
2. Bhattacharya,D. and Cheng,J. (2015) De novo protein conformational sampling using a probabilistic graphical model. Sci. Rep., 5, 1-13.
3. Boomsma,W. et al. (2008) A generative, probabilistic model of local protein structure. Proc. Natl. Acad. Sci. U. S. A., 105, 8932-8937.
4. Gront,D. et al. (2011) Generalized fragment picking in Rosetta: design, protocols and applications. PloS One, 6, e23294.
5. Hamelryck,T. et al. (2006) Sampling realistic protein conformations using local structural bias. PLoS Comput. Biol., 2, 1121-1133.
6. Jones,D.T. (1999) Protein secondary structure prediction based on positionspecific scoring matrices. J. Mol. Biol., 292, 195-202.
7. Kalev,I. and Habeck,M. (2011) HHfrag: HMM-based fragment detection using HHpred. Bioinformatics, 27, 3110-3116.
8. Kolodny,R. and Levitt,M. (2003) Protein decoy assembly using short fragments under geometric constraints. Biopolymers, 68, 278-285.
9. Mardia,K.V. and Jupp,P.E. (2009) Directional Statistics. John Wiley & Sons, London, UK.
10. Mardia,K.V. et al. (2007) Protein bioinformatics and mixtures of bivariate von Mises distributions for angular data. Biometrics, 63, 505-512.
11. Simons,K.T. et al. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol., 268, 209-225.
12. Zhang,Y. and Skolnick,J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins: Struct. Funct. Bioinf., 57, 702-710.