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Results: 1 to 20 of 110

1.

The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement.

Pawlowski M, Bujnicki JM.

BMC Bioinformatics. 2012 Nov 5;13:289. doi: 10.1186/1471-2105-13-289.

PMID:
23126528
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

The JCSG MR pipeline: optimized alignments, multiple models and parallel searches.

Schwarzenbacher R, Godzik A, Jaroszewski L.

Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):133-40. Epub 2007 Dec 5.

PMID:
18094477
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

MetaMQAP: a meta-server for the quality assessment of protein models.

Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM.

BMC Bioinformatics. 2008 Sep 29;9:403. doi: 10.1186/1471-2105-9-403.

PMID:
18823532
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

An iterative self-refining and self-evaluating approach for protein model quality estimation.

Wang Z, Cheng J.

Protein Sci. 2012 Jan;21(1):142-51. doi: 10.1002/pro.764. Epub 2011 Nov 23.

PMID:
22057943
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Evaluating the usefulness of protein structure models for molecular replacement.

Giorgetti A, Raimondo D, Miele AE, Tramontano A.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii72-6.

PMID:
16204129
[PubMed - indexed for MEDLINE]
Free Article
6.

Prediction of global and local model quality in CASP7 using Pcons and ProQ.

Wallner B, Elofsson A.

Proteins. 2007;69 Suppl 8:184-93.

PMID:
17894353
[PubMed - indexed for MEDLINE]
7.

Neural network pairwise interaction fields for protein model quality assessment and ab initio protein folding.

Martin AJ, Mirabello C, Pollastri G.

Curr Protein Pept Sci. 2011 Sep;12(6):549-62.

PMID:
21787307
[PubMed - indexed for MEDLINE]
8.

The importance of alignment accuracy for molecular replacement.

Schwarzenbacher R, Godzik A, Grzechnik SK, Jaroszewski L.

Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1229-36. Epub 2004 Jun 22.

PMID:
15213384
[PubMed - indexed for MEDLINE]
9.

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.

Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N.

J Struct Funct Genomics. 2012 Jun;13(2):81-90. doi: 10.1007/s10969-012-9129-3. Epub 2012 Mar 15.

PMID:
22418934
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Benchmarking consensus model quality assessment for protein fold recognition.

McGuffin LJ.

BMC Bioinformatics. 2007 Sep 18;8:345.

PMID:
17877795
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Improvement of 3D protein models using multiple templates guided by single-template model quality assessment.

Buenavista MT, Roche DB, McGuffin LJ.

Bioinformatics. 2012 Jul 15;28(14):1851-7. doi: 10.1093/bioinformatics/bts292. Epub 2012 May 15.

PMID:
22592378
[PubMed - indexed for MEDLINE]
Free Article
12.

Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.

Koliński A, Bujnicki JM.

Proteins. 2005;61 Suppl 7:84-90.

PMID:
16187348
[PubMed - indexed for MEDLINE]
13.

Sub-AQUA: real-value quality assessment of protein structure models.

Yang YD, Spratt P, Chen H, Park C, Kihara D.

Protein Eng Des Sel. 2010 Aug;23(8):617-32. doi: 10.1093/protein/gzq030. Epub 2010 Jun 4.

PMID:
20525730
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Molecular replacement then and now.

Scapin G.

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2266-75. doi: 10.1107/S0907444913011426. Epub 2013 Oct 18. Review.

PMID:
24189239
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Molecular replacement using ab initio polyalanine models generated with ROSETTA.

Rigden DJ, Keegan RM, Winn MD.

Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1288-91. doi: 10.1107/S0907444908033192. Epub 2008 Nov 18.

PMID:
19018106
[PubMed - indexed for MEDLINE]
16.

Assessment of CASP7 predictions in the high accuracy template-based modeling category.

Read RJ, Chavali G.

Proteins. 2007;69 Suppl 8:27-37.

PMID:
17894351
[PubMed - indexed for MEDLINE]
17.

Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments.

McGuffin LJ, Roche DB.

Bioinformatics. 2010 Jan 15;26(2):182-8. doi: 10.1093/bioinformatics/btp629. Epub 2009 Nov 6.

PMID:
19897565
[PubMed - indexed for MEDLINE]
Free Article
18.

Improving the quality of protein structure models by selecting from alignment alternatives.

Sommer I, Toppo S, Sander O, Lengauer T, Tosatto SC.

BMC Bioinformatics. 2006 Jul 27;7:364.

PMID:
16872519
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates.

Pandit SB, Skolnick J.

Proteins. 2010 Oct;78(13):2769-80. doi: 10.1002/prot.22791.

PMID:
20635423
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Improved technologies now routinely provide protein NMR structures useful for molecular replacement.

Mao B, Guan R, Montelione GT.

Structure. 2011 Jun 8;19(6):757-66. doi: 10.1016/j.str.2011.04.005.

PMID:
21645849
[PubMed - indexed for MEDLINE]
Free PMC Article

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