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Items: 1 to 20 of 143

1.

Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL.

Dunbrack RL Jr.

Proteins. 1999;Suppl 3:81-7.

PMID:
10526356
2.

Large-scale comparison of protein sequence alignment algorithms with structure alignments.

Sauder JM, Arthur JW, Dunbrack RL Jr.

Proteins. 2000 Jul 1;40(1):6-22.

PMID:
10813826
3.

Assessment of comparative modeling in CASP2.

Martin AC, MacArthur MW, Thornton JM.

Proteins. 1997;Suppl 1:14-28.

PMID:
9485491
4.

Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments.

Friedberg I, Kaplan T, Margalit H.

Protein Sci. 2000 Nov;9(11):2278-84.

5.

Sequence to structure alignment in comparative modeling using PrISM.

Yang AS, Honig B.

Proteins. 1999;Suppl 3:66-72.

PMID:
10526354
7.

Increased detection of structural templates using alignments of designed sequences.

Larson SM, Garg A, Desjarlais JR, Pande VS.

Proteins. 2003 May 15;51(3):390-6.

PMID:
12696050
8.
9.

Using CLUSTAL for multiple sequence alignments.

Higgins DG, Thompson JD, Gibson TJ.

Methods Enzymol. 1996;266:383-402.

PMID:
8743695
10.
11.

Improving the quality of twilight-zone alignments.

Jaroszewski L, Rychlewski L, Godzik A.

Protein Sci. 2000 Aug;9(8):1487-96.

12.

ESyPred3D: Prediction of proteins 3D structures.

Lambert C, LĂ©onard N, De Bolle X, Depiereux E.

Bioinformatics. 2002 Sep;18(9):1250-6.

13.

Fold recognition using sequence and secondary structure information.

Koretke KK, Russell RB, Copley RR, Lupas AN.

Proteins. 1999;Suppl 3:141-8.

PMID:
10526363
14.

SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling.

Wang Q, Canutescu AA, Dunbrack RL Jr.

Nat Protoc. 2008;3(12):1832-47. doi: 10.1038/nprot.2008.184.

15.

An iterative structure-assisted approach to sequence alignment and comparative modeling.

Burke DF, Deane CM, Nagarajaram HA, Campillo N, Martin-Martinez M, Mendes J, Molina F, Perry J, Reddy BV, Soares CM, Steward RE, Williams M, Carrondo MA, Blundell TL, Mizuguchi K.

Proteins. 1999;Suppl 3:55-60.

PMID:
10526352
17.

Modeling structurally variable regions in homologous proteins with rosetta.

Rohl CA, Strauss CE, Chivian D, Baker D.

Proteins. 2004 May 15;55(3):656-77.

PMID:
15103629
18.

Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles.

Kundrotas PJ, Lensink MF, Alexov E.

Int J Biol Macromol. 2008 Aug 15;43(2):198-208. doi: 10.1016/j.ijbiomac.2008.05.004.

PMID:
18572239
19.

Enhanced genome annotation using structural profiles in the program 3D-PSSM.

Kelley LA, MacCallum RM, Sternberg MJ.

J Mol Biol. 2000 Jun 2;299(2):499-520.

PMID:
10860755
20.

AS2TS system for protein structure modeling and analysis.

Zemla A, Zhou CE, Slezak T, Kuczmarski T, Rama D, Torres C, Sawicka D, Barsky D.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W111-5.

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