DOI: 10.1016/s0022-2836(03)00323-1. A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics

A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics

10.1016/s0022-2836(03)00323-1

Crossref journal-article

Elsevier BV

Journal of Molecular Biology (78)

Bibliography

Keasar, C., & Levitt, M. (2003). A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics. Journal of Molecular Biology, 329(1), 159â174.

Authors 2

Chen Keasar (first)
Michael Levitt (additional)

References 25 Referenced 74

10.1038/253694a0 / Nature / Computer simulation of protein folding by Levitt (1975)
10.1073/pnas.72.4.1221 / Proc. Natl Acad. Sci. USA / Assessment of some problems associated with prediction of the three-dimensional structure of a protein from its amino-acid sequence by Burgess (1975)
10.1002/(SICI)1097-0134(1999)37:3+<186::AID-PROT23>3.0.CO;2-D / Proteins: Struct. Funct. Genet. / Improved ab initio predictions with a simplified, flexible geometry model by Osguthorpe (1999)
10.1002/(SICI)1097-0134(1999)37:3+<204::AID-PROT26>3.0.CO;2-F / Proteins: Struct. Funct. Genet. / Calculation of protein conformation by global optimization of a potential energy function by Lee (1999)
10.1126/science.220.4598.671 / Science / Optimization by simulated annealing by Kirkpatrick (1983)
10.1006/jmbi.1997.1010 / J. Mol. Biol. / Protein folding simulations with genetic algorithms and a detailed molecular description by Pedersen (1997)
10.1021/j100345a090 / J. Phys. Chem. / The multiple minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method by Piela (1989)
10.1006/jmbi.1996.0256 / J. Mol. Biol. / Energy functions that discriminate X-ray and near-native folds from well-constructed decoys by Park (1996)
10.1016/0022-2836(94)90040-X / J. Mol. Biol. / Exploring conformational space with a simple lattice model for protein structure by Hinds (1994)
10.1006/jmbi.1995.0311 / J. Mol. Biol. / The complexity and accuracy of discrete state models of protein structure by Park (1995)
10.1006/jmbi.2000.4290 / J. Mol. Biol. / A novel method for sampling alpha-helical protein backbones by Fain (2001)
10.1002/(SICI)1097-0134(19980801)32:2<211::AID-PROT7>3.0.CO;2-N / Proteins: Struct. Funct. Genet. / Recognition of native structure from complete enumeration of low-resolution models with constraints by Ozkan (1998)
10.1016/0959-440X(95)80082-4 / Curr. Opin. Struct. Biol. / Statistics of sequence–structure threading by Bryant (1995)
10.1006/jmbi.2000.4459 / J. Mol. Biol. / Prospects for ab initio protein structural genomics by Simons (2001)
10.1002/1096-987X(200102)22:3<339::AID-JCC1006>3.0.CO;2-R / J. Comput. Chem. / Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions by Betancourt (2001)
10.1016/S1359-0278(98)00045-5 / Fold. Des. / Efficient dynamics in the space of contact maps by Vendruscolo (1998)
10.1093/comjnl/13.3.317 / Comput. J. / New approach to variable metric algorithms by Fletcher (1970)
10.1016/S0022-2836(83)80129-6 / J. Mol. Biol. / Protein folding by restrained energy minimization and molecular dynamics by Levitt (1983)
10.1063/1.477748 / J. Chem. Phys. / Pairwise contact potentials are unsuitable for protein folding1 by Vendruscolo (1998)
10.1016/S1359-0278(98)00051-0 / Fold. Des. / Empirical modifications to the Amber/OPLS potential for predicting the solution conformations of cyclic peptides by vacuum calculations by Keasar (1998)
10.1006/jmbi.2000.3835 / J. Mol. Biol. / Ab initio construction of protein tertiary structures using a hierarchical approach by Xia (2000)
10.1002/(SICI)1097-0134(1999)37:3+<177::AID-PROT22>3.0.CO;2-E / Proteins: Struct. Funct. Genet. / Ab initio folding of proteins using restraints derived from evolutionary information by Ortiz (1999)
10.1002/1097-0134(20010401)43:1<1::AID-PROT1012>3.0.CO;2-A / Proteins: Struct. Funct. Genet. / Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation by Bonneau (2001)
10.1006/jmbi.1997.1479 / J. Mol. Biol. / An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction by Samudrala (1998)
10.1002/elps.1150181505 / Electrophoresis / SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling by Guex (1997)

Dates

Type	When
Created	22 years, 3 months ago (May 12, 2003, 10:21 p.m.)
Deposited	6 years, 5 months ago (March 21, 2019, 9:23 a.m.)
Indexed	1 year ago (Aug. 12, 2024, 9:55 a.m.)
Issued	22 years, 3 months ago (May 1, 2003)
Published	22 years, 3 months ago (May 1, 2003)
Published Print	22 years, 3 months ago (May 1, 2003)

Funders 0

None

BibTeX

@article{Keasar_2003, title={A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics}, volume={329}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/s0022-2836(03)00323-1}, DOI={10.1016/s0022-2836(03)00323-1}, number={1}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Keasar, Chen and Levitt, Michael}, year={2003}, month=may, pages={159–174} }

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