Biomedical Engineering Reference
In-Depth Information
[83] P. Bradley, D. Chivian, J. Meiler, K. M. Misura, C. A. Rohl, W. R. Schief,
W. J. Wedemeyer, O. Schueler-Furman, P. Murphy, J. Schonbrun, C. E. Strauss
and D. Baker, Rosetta predictions in CASP5: Successes, failures, and prospects for
complete automation, Proteins , 53 Suppl. 6, 457-468 (2003).
[84] P. Bradley, L. Malmstrom, B. Qian, J. Schonbrun, D. Chivian, D. E. Kim, J. Meiler,
K. M. Misura and D. Baker, Free modeling with Rosetta in CASP6, Proteins , 61
Suppl. 7, 128-134 (2005).
[85] R. Bonneau, C. E. Strauss, C. A. Rohl, D. Chivian, P. Bradley, L. Malmstrom,
T. Robertson and D. Baker, De novo prediction of three-dimensional structures for
major protein families, J. Mol. Biol. , 322, 65-78 (2002).
[86] B. Kuhlman, G. Dantas, G. C. Ireton, G. Varani, B. L. Stoddard and D. Baker, Design of a
novel globular protein fold with atomic-level accuracy, Science , 302, 1364-1368 (2003).
[87] G. L. Butterfoss and B. Kuhlman, Computer-based design of novel protein struc-
tures, Ann. Rev. Biophys. & Biomol. Struct. , 35, 49-65 (2006).
[88] J. Meiler and D. Baker, Rosettaligand: Protein-small molecule docking with full
side-chain flexibility, Proteins , 65, 538-548 (2006).
[89] O. Schueler-Furman, C. Wang and D. Baker, Progress in protein-protein docking:
Atomic resolution predictions in the CAPRI experiment using Rosettadock with an
improved treatment of side-chain flexibility, Proteins , 60, 187-194 (2005).
[90] J. J. Gray, S. Moughon, C. Wang, O. Schueler-Furman, B. Kuhlman, C. A. Rohl and
D. Baker, Protein-protein docking with simultaneous optimization of rigid-body
displacement and side-chain conformations, J. Mol. Biol. , 331, 281-299 (2003).
[91] J. Desmet, M. De Maeyer, B. Hazes and I. Lasters, The dead-end elimination
theorem and its use in protein side-chain positioning, Nature , 356, 539-542 (1992).
[92] A. R. Leach, Ligand docking to proteins with discrete side-chain flexibility, J. Mol.
Biol. , 235, 345-356 (1994).
[93] M. De Maeyer, J. Desmet and I. Lasters, The dead-end elimination theorem:
Mathematical aspects, implementation, optimizations, evaluation, and perfor-
mance, Methods in Molecular Biology , 143, 265-304 (2000).
[94] A. A. Canutescu, A. A. Shelenkov and R. L. Dunbrack, Jr., A graph-theory algorithm
for rapid protein side-chain prediction, Protein Sci. , 12, 2001-2014 (2003).
[95] B. Kuhlman and D. Baker, Native protein sequences are close to optimal for their
structures, PNAS , 97, 10383-10388 (2000).
[96] C. Wang, O. Schueler-Furman and D. Baker, Improved side-chain modeling for
protein-protein docking, Protein Sci. , 14, 1328-1339 (2005).
[97] M. J. Bower, F. E. Cohen and R. L. Dunbrack, Jr., Prediction of protein side-chain
rotamers from a backbone-dependent rotamer library: A new homology modeling
tool, J. Mol. Biol. , 267, 1268-1282 (1997).
[98] R. L. Dunbrack, Jr., Comparative modeling of CASP3 targets using psi-blast and
SCWRL, Proteins , Suppl. 3, 81-87 (1999).
[99] G. V. Nikiforovich, V. J. Hruby, O. Prakash and C. A. Gehrig, Topographical
requirements for delta-selective opioid peptides, Biopolymers , 31, 941-955 (1991).
[100] C. C. Bleul, M. Farzan, H. Choe, C. Parolin, I. Clark-Lewis, J. Sodroski and
T. A. Springer, The lymphocyte chemoattractant SDF-1 is a ligand for lestr/fusin
and blocks HIV-1 entry, Nature , 382, 829-833 (1996).
[101] E. Oberlin, A. Amara, F. Bachelerie, C. Bessia, J. L. Virelizier, F. Arenzana-
Seisdedos, O. Schwartz, J. M. Heard, I. Clark-Lewis, D. F. Legler, M. Loetscher,
M. Baggiolini and B. Moser, The CXC chemokine SDF-1 is the ligand for lestr/
Search WWH ::




Custom Search