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Items: 1 to 20 of 119

1.

Protein structure prediction and model quality assessment.

Kryshtafovych A, Fidelis K.

Drug Discov Today. 2009 Apr;14(7-8):386-93. doi: 10.1016/j.drudis.2008.11.010. Epub 2009 Jan 15. Review.

3.

Quality assessment of protein model-structures based on structural and functional similarities.

Konopka BM, Nebel JC, Kotulska M.

BMC Bioinformatics. 2012 Sep 21;13:242. doi: 10.1186/1471-2105-13-242.

4.

Template-based protein structure modeling.

Fiser A.

Methods Mol Biol. 2010;673:73-94. doi: 10.1007/978-1-60761-842-3_6. Review.

5.

State-of-the-art bioinformatics protein structure prediction tools (Review).

Pavlopoulou A, Michalopoulos I.

Int J Mol Med. 2011 Sep;28(3):295-310. doi: 10.3892/ijmm.2011.705. Epub 2011 May 23. Review.

PMID:
21617841
6.

A generalized affine gap model significantly improves protein sequence alignment accuracy.

Zachariah MA, Crooks GE, Holbrook SR, Brenner SE.

Proteins. 2005 Feb 1;58(2):329-38.

PMID:
15562515
7.
8.

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

Moult J.

Curr Opin Struct Biol. 2005 Jun;15(3):285-9. Review.

PMID:
15939584
9.

Computational methods for protein secondary structure prediction using multiple sequence alignments.

Heringa J.

Curr Protein Pept Sci. 2000 Nov;1(3):273-301. Review.

PMID:
12369910
10.

From analysis of protein structural alignments toward a novel approach to align protein sequences.

Sunyaev SR, Bogopolsky GA, Oleynikova NV, Vlasov PK, Finkelstein AV, Roytberg MA.

Proteins. 2004 Feb 15;54(3):569-82.

PMID:
14748004
11.

Principles, challenges and advances in ab initio protein structure prediction.

Jothi A.

Protein Pept Lett. 2012 Nov;19(11):1194-204.

PMID:
22587787
12.

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. Epub 2008 May 21.

PMID:
18572239
13.

Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment.

Shatsky M, Nussinov R, Wolfson HJ.

Methods Mol Biol. 2008;413:125-46.

PMID:
18075164
14.

Protein structure prediction: inroads to biology.

Petrey D, Honig B.

Mol Cell. 2005 Dec 22;20(6):811-9. Review.

15.
16.

Integrating protein secondary structure prediction and multiple sequence alignment.

Simossis VA, Heringa J.

Curr Protein Pept Sci. 2004 Aug;5(4):249-66. Review.

PMID:
15320732
17.

Progress in protein structure prediction: assessment of CASP3.

Sternberg MJ, Bates PA, Kelley LA, MacCallum RM.

Curr Opin Struct Biol. 1999 Jun;9(3):368-73. Review.

PMID:
10361096
18.

An introduction to protein contact prediction.

Hamilton N, Huber T.

Methods Mol Biol. 2008;453:87-104. doi: 10.1007/978-1-60327-429-6_3.

PMID:
18712298
19.

A spectral approach to protein structure alignment.

Shibberu Y, Holder A.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):867-75. doi: 10.1109/TCBB.2011.24.

PMID:
21301031
20.

Protein structure homology modeling using SWISS-MODEL workspace.

Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T.

Nat Protoc. 2009;4(1):1-13. doi: 10.1038/nprot.2008.197.

PMID:
19131951
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