1.
Hamblin,
D. M. Standley, M. Rogers, A. Stechmann, A.J. Roger, R. Maytum, and M. van der
Giezen: ÒAn electrostatic gatekeeper controls nucleotide specificity in
succinyl-CoA synthetaseÓ (in
preparation).
2.
D.
M. Standley, H. Toh, and H. Nakamura: "Functional annotation by
sequence-weighted structure alignments: Statistical analysis and case studies
from the Protein 3000 structural genomics project in Japan," (Submitted to
Proteins: Struct. Funct. Bioinfo.).
3.
E.
Kanamori, Y. Murakami, Y. Tsuchiya, D. Standley, K. Kinoshita, and H. Nakamura:
ÒDocking of protein molecular surfaces with
evolutionary trace analysis,Ó Proteins:
Struct. Funct. Bioinfo. 2007 (in press).
4.
D.
M. Standley, H. Toh, and H. Nakamura: ÒASH structure
alignment package: Sensitivity and selectivity in domain classification,Ó BMC Bioinformatics 2007, 8:116.
5.
D. M. Standley, Y. Yonezawa, Y. Goto, and H. Nakamura: ÒFlexible
Docking of an Amyloid-forming peptide from b2-microglobulin,Ó FEBS Letters, 2006; 580:6199-6205.
6.
P. Gou, G.T. Hanke, Y. Kimata-Ariga, D. M. Standley, A. Kubo, I.
Taniguchi, H. Nakamura, and T. Hase: ÒHigher Order Structure Contributes to
Specific Differences in Redox Potential and Electron Transfer Efficiency of
Root and Leaf Ferredoxins,Ó Biochemistry, 2006
45(48):14389-14396.
7.
H. M. Berman, S. K. Burley, W. Chiu, A. Sali, A. Adzhubei, P. E.
Bourne, S. H. Bryant, R. L. Dunbrack, Jr., K. Fidelis, J. Frank, A. Godzik, K.
Henrick, A. Joachimiak, B. Heymann, D. Jones, J. L. Markley, J. Moult, G. T.
Montelione, C. Orengo, M. T. Rossmann, B. Rost, H. Saibil, T. Schwede, D. M.
Standley, and J. D. Westbrook: ÒOutcome of a Workshop on Archiving Structural
Models of Biological Macromodels,Ó Structure, 2006; 14:1211-1217.
8.
D.
M. Standley, H. Toh, and H. Nakamura: "GASH: A Server for Maximizing the
Number of Equivalent Residues between Two Structures," BMC
Bioinformatics,
2005; 6:221.
9.
D.
M. Standley, H. Toh, and H. Nakamura: "Detecting Local Structural
Similarity in Proteins by Maximizing the Number of Equivalent Residues," Proteins:
Struct. Funct. Bioinfo. 2004; 57, 381-391.
10.
D. M. Standley, V. A. Eyrich, Y. An, D. L. Pincus, and R. A.
Friesner: ÒProtein Structure Prediction Using a Combination of Sequence-based Alignment,
Constrained Energy Minimization, and Structural AlignmentÓ Proteins, 2001; Suppl 5:133-139.
11. V. A. Eyrich, D. M. Standley, and R. A. Friesner: "Ab Initio Protein Structure Prediction Using a Size-Dependent Tertiary Folding Potential,Ó in Advances in Chemical Physics:ÒComputational Methods for Protein Folding,Ó 2001; 120, edited by R. A. Friesner and S. A. Rice, Wiley Interscience.
12.
V.
A. Eyrich, D. M. Standley, and R. A. Friesner: ÒGlobal Optimization and
Sampling in the Context of Tertiary Structure Prediction: A Comparison of Two
Algorithms,Ó in Optimization in Computational Chemistry and Molecular
Biology,
2000; edited by CA. Floudas and P. M. Pardalos, Kluwer, Academic Publishers
B.V., 57-71.
13.
V.
A. Eyrich, D. M. Standley, and R. A. Friesner: "Prediction of Protein
Tertiary Structure to Low Resolution: Performance for a Large and Structurally
Diverse Test Set," J. Mol. Biol., 1999; 288, 725-742.
14.
V. A. Eyrich D.M. Standley. A. K. Felts, and R. A.
Friesner: "Protein Tertiary Structure Prediction Using a Branch and Bound
Algorithm," Proteins: Struct. Funct. Genet., 1999; 35, 41-57.
15.
D.
M. Standley, V. A. Eyrich, A. K. Felts, R. A. Friesner, and A. E. McDermott:
"A Branch and Bound Algorithm for Protein Structure Refinement from Sparse
NMR Data Sets," J. Mol. Biol., 1999; 285, 1689-1708.
16.
D.
M. Standley, J.R. Gunn, R. A. Friesner, and A. E. McDermott: "Tertiary
Structure Prediction of Mixed a/b Proteins via Energy
Minimization," Proteins: Struct. Funct. Genet., 1998; 33, 240-252.