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Results: 1 to 20 of 98

1.

Native protein sequences are close to optimal for their structures.

Kuhlman B, Baker D.

Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10383-8. Erratum in: Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13460.

PMID:
10984534
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

The native sequence determines sidechain packing in a protein, but does optimal sidechain packing determine the native sequence?

Koehl P, Delarue M.

Pac Symp Biocomput. 1997:198-209.

PMID:
9390292
[PubMed - indexed for MEDLINE]
3.

Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space.

Fromer M, Yanover C.

Proteins. 2009 May 15;75(3):682-705. doi: 10.1002/prot.22280.

PMID:
19003998
[PubMed - indexed for MEDLINE]
5.

Folding free energy function selects native-like protein sequences in the core but not on the surface.

Jaramillo A, Wernisch L, Héry S, Wodak SJ.

Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13554-9. Epub 2002 Oct 4.

PMID:
12368470
[PubMed - indexed for MEDLINE]
Free PMC Article
6.
7.

Energetics of the native and non-native states of the glycophorin transmembrane helix dimer.

Mottamal M, Zhang J, Lazaridis T.

Proteins. 2006 Mar 1;62(4):996-1009.

PMID:
16395713
[PubMed - indexed for MEDLINE]
8.

De novo protein design. II. Plasticity in sequence space.

Koehl P, Levitt M.

J Mol Biol. 1999 Nov 12;293(5):1183-93.

PMID:
10547294
[PubMed - indexed for MEDLINE]
9.

Recapitulation of protein family divergence using flexible backbone protein design.

Saunders CT, Baker D.

J Mol Biol. 2005 Feb 18;346(2):631-44. Epub 2005 Jan 8.

PMID:
15670610
[PubMed - indexed for MEDLINE]
10.

Protein topology and stability define the space of allowed sequences.

Koehl P, Levitt M.

Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1280-5. Epub 2002 Jan 22.

PMID:
11805293
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Automatic protein design with all atom force-fields by exact and heuristic optimization.

Wernisch L, Hery S, Wodak SJ.

J Mol Biol. 2000 Aug 18;301(3):713-36.

PMID:
10966779
[PubMed - indexed for MEDLINE]
12.

The identification of conserved interactions within the SH3 domain by alignment of sequences and structures.

Larson SM, Davidson AR.

Protein Sci. 2000 Nov;9(11):2170-80.

PMID:
11152127
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

De novo protein design. I. In search of stability and specificity.

Koehl P, Levitt M.

J Mol Biol. 1999 Nov 12;293(5):1161-81.

PMID:
10547293
[PubMed - indexed for MEDLINE]
14.

Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space.

Miyazawa S, Jernigan RL.

Proteins. 2003 Jan 1;50(1):35-43.

PMID:
12471597
[PubMed - indexed for MEDLINE]
15.

Design of amino acid sequences to fold into C(alpha)-model proteins.

Amatori A, Tiana G, Sutto L, Ferkinghoff-Borg J, Trovato A, Broglia RA.

J Chem Phys. 2005 Aug 1;123(5):054904.

PMID:
16108690
[PubMed - indexed for MEDLINE]
16.

Solution structure of a de novo protein from a designed combinatorial library.

Wei Y, Kim S, Fela D, Baum J, Hecht MH.

Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13270-3. Epub 2003 Oct 30.

PMID:
14593201
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

De novo design of the hydrophobic cores of proteins.

Desjarlais JR, Handel TM.

Protein Sci. 1995 Oct;4(10):2006-18.

PMID:
8535237
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.

Abagyan R, Totrov M.

J Mol Biol. 1994 Jan 21;235(3):983-1002.

PMID:
8289329
[PubMed - indexed for MEDLINE]
19.

Improved recognition of native-like protein structures using a family of designed sequences.

Koehl P, Levitt M.

Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):691-6. Epub 2002 Jan 8.

PMID:
11782533
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Determination of the conformation of folding initiation sites in proteins by computer simulation.

Avbelj F, Moult J.

Proteins. 1995 Oct;23(2):129-41.

PMID:
8592695
[PubMed - indexed for MEDLINE]

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