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Results: 1 to 20 of 53

References for PMC Articles for PubMed (Select 20462859)

1.

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.

Potapov V, Cohen M, Schreiber G.

Protein Eng Des Sel. 2009 Sep;22(9):553-60. doi: 10.1093/protein/gzp030. Epub 2009 Jun 26.

2.

A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T.

PLoS Comput Biol. 2009 May;5(5):e1000393. doi: 10.1371/journal.pcbi.1000393. Epub 2009 May 29.

3.

RosettaAntibody: antibody variable region homology modeling server.

Sircar A, Kim ET, Gray JJ.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W474-9. doi: 10.1093/nar/gkp387. Epub 2009 May 20.

4.

Assessment of the optimization of affinity and specificity at protein-DNA interfaces.

Ashworth J, Baker D.

Nucleic Acids Res. 2009 Jun;37(10):e73. doi: 10.1093/nar/gkp242. Epub 2009 Apr 23.

5.

Predicting free energy changes using structural ensembles.

Benedix A, Becker CM, de Groot BL, Caflisch A, Böckmann RA.

Nat Methods. 2009 Jan;6(1):3-4. doi: 10.1038/nmeth0109-3. No abstract available.

PMID:
19116609
6.

Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations.

Liang S, Li L, Hsu WL, Pilcher MN, Uversky V, Zhou Y, Dunker AK, Meroueh SO.

Biochemistry. 2009 Jan 20;48(2):399-414. doi: 10.1021/bi8017043.

7.

Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design.

Humphris EL, Kortemme T.

Structure. 2008 Dec 10;16(12):1777-88. doi: 10.1016/j.str.2008.09.012.

8.

FunHunt: model selection based on energy landscape characteristics.

London N, Schueler-Furman O.

Biochem Soc Trans. 2008 Dec;36(Pt 6):1418-21. doi: 10.1042/BST0361418.

PMID:
19021567
9.

Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles.

Chaudhury S, Gray JJ.

J Mol Biol. 2008 Sep 12;381(4):1068-87. doi: 10.1016/j.jmb.2008.05.042. Epub 2008 May 24.

10.

Algorithm for backrub motions in protein design.

Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR.

Bioinformatics. 2008 Jul 1;24(13):i196-204. doi: 10.1093/bioinformatics/btn169.

11.

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.

Lange OF, Lakomek NA, Farès C, Schröder GF, Walter KF, Becker S, Meiler J, Grubmüller H, Griesinger C, de Groot BL.

Science. 2008 Jun 13;320(5882):1471-5. doi: 10.1126/science.1157092.

12.

A simple model of backbone flexibility improves modeling of side-chain conformational variability.

Friedland GD, Linares AJ, Smith CA, Kortemme T.

J Mol Biol. 2008 Jul 18;380(4):757-74. doi: 10.1016/j.jmb.2008.05.006. Epub 2008 May 11.

13.

Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction.

Smith CA, Kortemme T.

J Mol Biol. 2008 Jul 18;380(4):742-56. doi: 10.1016/j.jmb.2008.05.023. Epub 2008 May 17.

14.

The RosettaDock server for local protein-protein docking.

Lyskov S, Gray JJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W233-8. doi: 10.1093/nar/gkn216. Epub 2008 Apr 28.

15.

Macromolecular modeling with rosetta.

Das R, Baker D.

Annu Rev Biochem. 2008;77:363-82. doi: 10.1146/annurev.biochem.77.062906.171838. Review.

PMID:
18410248
16.

Kemp elimination catalysts by computational enzyme design.

Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D.

Nature. 2008 May 8;453(7192):190-5. doi: 10.1038/nature06879. Epub 2008 Mar 19.

PMID:
18354394
17.

De novo computational design of retro-aldol enzymes.

Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF 3rd, Hilvert D, Houk KN, Stoddard BL, Baker D.

Science. 2008 Mar 7;319(5868):1387-91. doi: 10.1126/science.1152692.

18.

A new twist in TCR diversity revealed by a forbidden alphabeta TCR.

McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK.

J Mol Biol. 2008 Feb 1;375(5):1306-19. Epub 2007 Nov 17.

19.

Design of multi-specificity in protein interfaces.

Humphris EL, Kortemme T.

PLoS Comput Biol. 2007 Aug;3(8):e164. Epub 2007 Jul 5.

20.

Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity.

Lengyel CS, Willis LJ, Mann P, Baker D, Kortemme T, Strong RK, McFarland BJ.

J Biol Chem. 2007 Oct 19;282(42):30658-66. Epub 2007 Aug 8.

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