DOI: 10.1016/j.jmb.2009.07.063. Sampling Bottlenecks in De novo Protein Structure Prediction

Sampling Bottlenecks in De novo Protein Structure Prediction

10.1016/j.jmb.2009.07.063

Crossref journal-article

Elsevier BV

Journal of Molecular Biology (78)

Bibliography

Kim, D. E., Blum, B., Bradley, P., & Baker, D. (2009). Sampling Bottlenecks in De novo Protein Structure Prediction. Journal of Molecular Biology, 393(1), 249â260.

Authors 4

David E. Kim (first)
Ben Blum (additional)
Philip Bradley (additional)
David Baker (additional)

References 28 Referenced 84

10.1002/prot.20729 / Proteins / Free modeling with Rosetta in CASP6 by Bradley (2005)
10.1002/prot.21636 / Proteins / Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home by Das (2007)
10.1126/science.1113801 / Science / Toward high-resolution de novo structure prediction for small proteins by Bradley (2005)
10.1002/prot.20376 / Proteins / Progress and challenges in high-resolution refinement of protein structure models by Misura (2005)
10.1006/jmbi.1996.0020 / J. Mol. Biol. / Automatic classification and analysis of αα-turn motifs in proteins by Wintjens (1996)
10.1073/pnas.0509355103 / Proc. Natl Acad. Sci. USA / Physically realistic homology models built with ROSETTA can be more accurate than their templates by Misura (2006)
10.1016/S0969-2126(97)00192-5 / Structure / Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis by Xu (1997)
10.1016/S0092-8674(00)80668-6 / Cell / Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome by Lewis (2000)
10.1073/pnas.82.21.7242 / Proc. Natl Acad. Sci. USA / Crystal and molecular structure of chymotrypsin inhibitor 2 from barley seeds in complex with subtilisin Novo by McPhalen (1985)
10.1128/JB.180.8.2257-2261.1998 / J. Bacteriol. / The yhhP gene encoding a small ubiquitous protein is fundamental for normal cell growth of Escherichia coli by Yamashino (1998)
10.1016/S0969-2126(97)00180-9 / Structure / The structure of an energy-coupling protein from bacteria, IIBcellobiose, reveals similarity to eukaryotic protein tyrosine phosphatases by van Montfort (1997)
10.1093/protein/gzi025 / Protein Eng. Des. Sel. / Ubiquitin folds through a highly polarized transition state by Went (2005)
10.1073/pnas.94.3.826 / Proc. Natl Acad. Sci. USA / The folding pathway of a protein at high resolution from microseconds to seconds by Nolting (1997)
10.1016/S1359-0278(96)00011-9 / Fold Des. / Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2 by Lopez-Hernandez (1996)
10.1006/jmbi.2000.4507 / J. Mol. Biol. / Towards understanding a molecular switch mechanism: thermodynamic and crystallographic studies of the signal transduction protein CheY by Sola (2000)
10.1073/pnas.052706099 / Proc. Natl Acad. Sci. USA / Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation by Richardson (2002)
10.1007/s10858-008-9288-5 / J. Biomol. NMR / De novo protein structure generation from incomplete chemical shift assignments by Shen (2009)
10.1002/pro.5560021004 / Protein Sci. / Identification, classification, and analysis of β-bulges in proteins by Chan (1993)
10.1002/prot.21133 / Proteins / Improved β-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation by Bradley (2006)
10.1006/jmbi.1997.0959 / J. Mol. Biol. / Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions by Simons (1997)
10.1002/(SICI)1097-0134(19990101)34:1<82::AID-PROT7>3.0.CO;2-A / Proteins / Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins by Simons (1999)
10.1126/science.1089427 / Science / Design of a novel globular protein fold with atomic-level accuracy by Kuhlman (2003)
10.1016/S0076-6879(04)83004-0 / Methods Enzymol. / Protein structure prediction using Rosetta by Rohl (2004)
10.1126/science.1112160 / Science / Progress in modeling of protein structures and interactions by Schueler-Furman (2005)
{'key': '10.1016/j.jmb.2009.07.063_bib25', 'first-page': '137', 'article-title': 'Feature selection methods for improving protein structure prediction with Rosetta', 'volume': '20', 'author': 'Blum', 'year': '2008', 'journal-title': 'NIPS'} / NIPS / Feature selection methods for improving protein structure prediction with Rosetta by Blum (2008)
10.1002/bip.360221211 / Biopolymers / Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features by Kabsch (1983)
10.1110/ps.0242703 / Protein Sci. / Cyclic coordinate descent: A robotics algorithm for protein loop closure by Canutescu (2003)
10.1006/jmbi.1999.3091 / J. Mol. Biol. / Protein secondary structure prediction based on position-specific scoring matrices by Jones (1999)

Dates

Type	When
Created	16 years, 1 month ago (July 29, 2009, 9:07 a.m.)
Deposited	5 years, 3 months ago (May 20, 2020, 10:07 p.m.)
Indexed	1 year, 1 month ago (Aug. 5, 2024, 1:12 p.m.)
Issued	15 years, 11 months ago (Oct. 1, 2009)
Published	15 years, 11 months ago (Oct. 1, 2009)
Published Print	15 years, 11 months ago (Oct. 1, 2009)

Funders 0

None

BibTeX

@article{Kim_2009, title={Sampling Bottlenecks in De novo Protein Structure Prediction}, volume={393}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/j.jmb.2009.07.063}, DOI={10.1016/j.jmb.2009.07.063}, number={1}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Kim, David E. and Blum, Ben and Bradley, Philip and Baker, David}, year={2009}, month=oct, pages={249–260} }

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