Biology Reference
In-Depth Information
51.
Park, B. and M. Levitt. Energy functions that discriminate x-ray and near
native folds from well-constructed decoys.
Journal of Molecular Biology
,
258:367-92, 1996.
52.
Meller, J. and R. Elber. Linear programming optimization and a double
statistical filter for protein threading protocols.
Proteins
, 45:241-61, 2001.
53.
Tobi, D. and R. Elber. Distance-dependent, pair potential for protein folding:
results from linear optimization.
Proteins: Structure, Function, and Genetics
,
41:40-6, 2000.
54.
Tobi, D., G. Shafran, N. Linial and R. Elber. On the design and analysis of
protein folding potentials.
Proteins
, 40:71-85, 2000.
55.
Loose, C., J. L. Klepeis and C. A. Floudas. A new pairwise folding poten-
tial based on improved decoy generation and side-chain packing.
Proteins:
Structure, Function, and Bioinformatics
, 54:303-14, 2004.
56.
Floudas, C. A.
Nonlinear and Mixed-Integer Optimization: Fundamentals and
Applications
. Oxford University Press, New York, 1995.
57.
CPLEX.
Using the CPLEX Callable Library
. ILOG, Inc., Mountain View,
Cal., 1997.
58.
Sherali, H. D. and W. P. Adams.
A Reformulation Linearization Technique for
Solving Discrete and Continuous Nonconvex Problems
. Kluwer Academic
Publishing, Boston, 1999.
59.
Klepeis, J. L., H. D. Schafroth, K. M. Westerberg and C. A. Floudas.
Deterministic global optimization and ab initio approaches for the struc-
ture prediction of polypeptides, dynamics of protein folding and
protein-protein interaction. In R. A. Friesner (Ed.),
Advances in Chemical
Physics
, Vol. 120 (pp. 254-457). Wiley, New York, 2002.
60.
Klepeis, J. L., C. A. Floudas, D. Morikis and J. Lambris. Predicting peptide
structures using NMR data and deterministic global optimization.
Journal
of Computational Chem
i
stry
, 20:1354-70, 1999.
61.
Klepeis, J. L. and C. A. Floudas. Ab initio tertiary structure prediction of
proteins.
Journal of Global Optimization
, 25:113-40, 2003.
62.
NĂ©methy, G., K. Gibson, K. Palmer, C. Yoon, G. Paterlini, A. Zagari,
S. Rumsey and H. Scheraga. Energy parameters in polypeptides. 10.
Improved geometrical parameters and nonbonded interactions for use in
the ECEPP/3 algorithm, with application to proline-containing peptides.
Journal of Physical Chemistry
, 96:6472-84, 1992.
63.
Adjiman, C., I. Androulakis and C. A. Floudas. A global optimization
method, aBB, for general twice-differentiable constrained NPLs. I.
Theoretical advances.
Computers and Chemical Engineering
, 22:1137, 1998.
64.
Adjiman, C., I. Androulakis and C. A. Floudas. A global optimization method,
aBB, for general twice-differentiable constrained NPLs. II. Implementtation
and computational results.
Computers and Chemical Engineering
, 22:1159, 1998.
65.
Adjiman, C., I. Androulakis and C. A. Floudas. Global optimization of
mixed-integer nonlinear problems.
AIChE Journal
, 46:1769-97, 2000.
66.
Klepeis, J. L. and C. A. Floudas. Free energy calculations for peptides via
deterministic global optimization
. Journal of Chemical Physics
, 110:7491-512,
1999.
67.
Floudas, C. A.
Deterministic Global Optimization: Theory, Methods and
Applications
. Kluwer Academic Publishers, Boston, 2000.
Search WWH ::
Custom Search