Biomedical Engineering Reference
In-Depth Information
45. Mandell, D.J., Coutsias, E.A., Kortemme, T.: Sub-angstrom accuracy in protein loop recon-
struction by robotics-inspired conformational sampling. Nat. Methods
6
, 551-552 (2009)
46. Ding, F., Tsao, D., Nie, H., Dokholyan, N.V.: Ab initio folding of proteins with all-atom
discrete molecular dynamics. Structure
16
, 1010-1018 (2008)
47. Kaufmann, K.W., Lemmon, G.H., Deluca, S.L., Sheehan, J.H., Meiler, J.: Practically useful:
what the Rosetta protein modeling suite can do for you. Biochemistry
49
, 2987-2998 (2010)
48. Feig, M., Karanicolas, J., Brooks, C.L. III.: MMTSB Tool Set: enhanced sampling and
multiscale modeling methods for applications in structural biology. J. Mol. Graph. Model
22
,
377-395 (2004)
49. Rotkiewicz, P., Skolnick, J.: Fast procedure for reconstruction of full-atom protein models from
reduced representations. J. Comput. Chem.
29
, 1460-1465 (2008)
50. Ramachandran, S., Kota, P., Ding, F., Dokholyan, N.V.: Automated minimization of steric
clashes in protein structures. Proteins
79
, 261-270 (2011)
51. Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E., Shakhnovich, E.I.: Discrete molecular dynam-
ics studies of the folding of a protein-like model. Fold Des.
3
, 577-587 (1998)
52. Zhang, Y., Skolnick, J.: Scoring function for automated assessment of protein structure
template quality. Proteins
57
, 702-710 (2004)
53. Sadreyev, R.I., Shi, S., Baker, D., Grishin, N.V.: Structure similarity measure with penalty for
close non-equivalent residues. Bioinformatics
25
, 1259-1263 (2009)
54. Eramian, D., Eswar, N., Shen, M.Y., Sali, A.: How well can the accuracy of comparative protein
structure models be predicted? Protein Sci.
17
, 1881-1893 (2008)
55. Benkert, P., Tosatto, S.C., Schomburg, D.: QMEAN: a comprehensive scoring function for
model quality assessment. Proteins
71
, 261-277 (2008)
56. Wallner,
B.,
Elofsson,
A.: Can
correct
protein
models
be identified?
Protein
Sci.
12
,
1073-1086 (2003)
57. Wallner, B., Elofsson, A.: Pcons5: combining consensus, structural evaluation and fold
recognition scores. Bioinformatics
21
, 4248-4254 (2005)
58. McGuffin, L.J., Roche, D.B.: Rapid model quality assessment for protein structure predictions
using the comparison of multiple models without structural alignments. Bioinformatics
26
,
182-188 (2010)
59. Cheng, J., Wang, Z., Tegge, A.N., Eickholt, J.: Prediction of global and local quality of CASP8
models by MULTICOM series. Proteins
77
(Suppl 9), 181-184 (2009)
60. Benkert, P., Schwede, T., Tosatto, S.C.: QMEANclust: estimation of protein model quality by
combining a composite scoring function with structural density information. BMC Struct. Biol.
9
, 35 (2009)
61. Hooft, R.W.W., Vriend, G., Sander, C., Abola, E.E.: Errors in protein structures. Nature
381
,
272-272 (1996)
62. Kota, P., Ding, F., Ramachandran, S., Dokholyan, N.V.: Gaia: automated quality assessment of
protein structure models. Bioinformatics
27
, 2209-2215 (2011)
63. Dunbrack, R.L., Jr., Cohen, F.E.: Bayesian statistical analysis of protein side-chain rotamer
preferences. Protein Sci.
6
, 1661-1681 (1997)
64. Davis, I.W., Leaver-Fay, A., Chen, V.B., Block, J.N., Kapral, G.J., Wang, X., Murray,
L.W., Arendall, W.B. III, Snoeyink, J., Richardson, J.S., et al.: MolProbity: all-atom
contacts and structure validation for proteins and nucleic acids. Nucliec. Acids Res.
35
,
W375-W383 (2007)
65. Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M.: PROCHECK: a pro-
gram to check the stereochemical quality of protein structures. J.Appl. Crystallogr.,
26
,
283-291 (1993)
66. Alber, F., Forster, F., Korkin, D., Topf, M., Sali, A.: Integrating diverse data for structure
determination of macromolecular assemblies. Annu. Rev. Biochem.
77
, 443-477 (2008)
67. Tung, C.S., Wall, M.E., Gallagher, S.C., Trewhella, J.: A model of troponin-I in complex with
troponin-C using hybrid experimental data: the inhibitory region is a beta-hairpin. Protein Sci.
9
, 1312-1326 (2000)
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