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Items: 1 to 20 of 90

1.

Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment.

Day R, Joo H, Chavan AC, Lennox KP, Chen YA, Dahl DB, Vannucci M, Tsai JW.

Comput Biol Chem. 2013 Feb;42:40-8. doi: 10.1016/j.compbiolchem.2012.10.008. Epub 2012 Nov 23.

2.

Template-based protein structure modeling using TASSER(VMT.).

Zhou H, Skolnick J.

Proteins. 2012 Feb;80(2):352-61. doi: 10.1002/prot.23183. Epub 2011 Nov 22.

3.

Protein structure modeling for CASP10 by multiple layers of global optimization.

Joo K, Lee J, Sim S, Lee SY, Lee K, Heo S, Lee IH, Lee SJ, Lee J.

Proteins. 2014 Feb;82 Suppl 2:188-95. doi: 10.1002/prot.24397. Epub 2013 Oct 24.

PMID:
23966235
4.

Recursive protein modeling: a divide and conquer strategy for Protein Structure Prediction and its case study in CASP9.

Cheng J, Eickholt J, Wang Z, Deng X.

J Bioinform Comput Biol. 2012 Jun;10(3):1242003. doi: 10.1142/S0219720012420036.

5.

A guide to template based structure prediction.

Qu X, Swanson R, Day R, Tsai J.

Curr Protein Pept Sci. 2009 Jun;10(3):270-85. Review.

PMID:
19519455
6.

A multi-template combination algorithm for protein comparative modeling.

Cheng J.

BMC Struct Biol. 2008 Mar 17;8:18. doi: 10.1186/1472-6807-8-18.

7.
8.

Constructing templates for protein structure prediction by simulation of protein folding pathways.

Kifer I, Nussinov R, Wolfson HJ.

Proteins. 2008 Nov 1;73(2):380-94. doi: 10.1002/prot.22073.

9.

eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures.

Brylinski M, Lingam D.

PLoS One. 2012;7(11):e50200. doi: 10.1371/journal.pone.0050200. Epub 2012 Nov 21.

10.

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field.

Krupa P, Mozolewska MA, Joo K, Lee J, Czaplewski C, Liwo A.

J Chem Inf Model. 2015 Jun 22;55(6):1271-81. doi: 10.1021/acs.jcim.5b00117. Epub 2015 May 22.

PMID:
25965196
11.

Modeling large regions in proteins: applications to loops, termini, and folding.

Adhikari AN, Peng J, Wilde M, Xu J, Freed KF, Sosnick TR.

Protein Sci. 2012 Jan;21(1):107-21. doi: 10.1002/pro.767. Epub 2011 Dec 5.

12.

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
13.

Target domain definition and classification in CASP8.

Tress ML, Ezkurdia I, Richardson JS.

Proteins. 2009;77 Suppl 9:10-7. doi: 10.1002/prot.22497.

14.

Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding.

Mishra A, Rao S, Mittal A, Jayaram B.

Biochim Biophys Acta. 2013 Aug;1834(8):1520-31. doi: 10.1016/j.bbapap.2013.04.023. Epub 2013 May 7.

PMID:
23665455
15.

Ab initio protein structure prediction of CASP III targets using ROSETTA.

Simons KT, Bonneau R, Ruczinski I, Baker D.

Proteins. 1999;Suppl 3:171-6.

PMID:
10526365
16.

Characterizing conserved structural contacts by pair-wise relative contacts and relative packing groups.

Holmes JB, Tsai J.

J Mol Biol. 2005 Dec 2;354(3):706-21. Epub 2005 Oct 18.

PMID:
16269154
17.

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.

Xu D, Zhang J, Roy A, Zhang Y.

Proteins. 2011;79 Suppl 10:147-60. doi: 10.1002/prot.23111. Epub 2011 Aug 23.

18.

Refinement of unreliable local regions in template-based protein models.

Park H, Seok C.

Proteins. 2012 Aug;80(8):1974-86. doi: 10.1002/prot.24086. Epub 2012 May 23.

PMID:
22488760
19.

Modeling CAPRI Targets 110 - 120 by Template-Based and Free Docking Using Contact Potential and Combined Scoring Function.

Kundrotas PJ, Anishchenko I, Badal VD, Das M, Dauzhenka T, Vakser IA.

Proteins. 2017 Sep 14. doi: 10.1002/prot.25380. [Epub ahead of print]

PMID:
28905425
20.

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