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Items: 1 to 20 of 78

1.

Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution.

Grahnen JA, Kubelka J, Liberles DA.

J Mol Evol. 2011 Aug;73(1-2):23-33. doi: 10.1007/s00239-011-9454-3.

PMID:
21800121
2.

High-quality protein backbone reconstruction from alpha carbons using Gaussian mixture models.

Moore BL, Kelley LA, Barber J, Murray JW, MacDonald JT.

J Comput Chem. 2013 Aug 15;34(22):1881-9. doi: 10.1002/jcc.23330.

PMID:
23703289
3.

Coarse-grained models for proteins.

Tozzini V.

Curr Opin Struct Biol. 2005 Apr;15(2):144-50. Review.

PMID:
15837171
4.

Error-estimation-guided rebuilding of de novo models increases the success rate of ab initio phasing.

Shrestha R, Simoncini D, Zhang KY.

Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1522-34. doi: 10.1107/S0907444912037961.

PMID:
23090401
5.
6.

Statistical potentials for improved structurally constrained evolutionary models.

Kleinman CL, Rodrigue N, Lartillot N, Philippe H.

Mol Biol Evol. 2010 Jul;27(7):1546-60. doi: 10.1093/molbev/msq047.

PMID:
20159780
7.

Conformation-dependent sequence design: evolutionary approach.

Chertovich AV, Govorun EN, Ivanov VA, Khalatur PG, Khokhlov AR.

Eur Phys J E Soft Matter. 2004 Jan;13(1):15-25.

PMID:
15024612
8.

Coarse-grained models of protein folding: toy models or predictive tools?

Clementi C.

Curr Opin Struct Biol. 2008 Feb;18(1):10-5. Review.

PMID:
18160277
9.

dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment.

Alden K, Veretnik S, Bourne PE.

BMC Bioinformatics. 2010 Jun 9;11:310. doi: 10.1186/1471-2105-11-310.

10.

FlexE: efficient molecular docking considering protein structure variations.

Claussen H, Buning C, Rarey M, Lengauer T.

J Mol Biol. 2001 Apr 27;308(2):377-95.

PMID:
11327774
11.

REvolver: modeling sequence evolution under domain constraints.

Koestler T, von Haeseler A, Ebersberger I.

Mol Biol Evol. 2012 Sep;29(9):2133-45. doi: 10.1093/molbev/mss078.

PMID:
22383532
12.

Meta-DP: domain prediction meta-server.

Saini HK, Fischer D.

Bioinformatics. 2005 Jun 15;21(12):2917-20.

PMID:
15840708
13.

Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis.

Buchete NV, Straub JE, Thirumalai D.

J Mol Graph Model. 2004 May;22(5):441-50.

PMID:
15099839
14.

A fast method for large-scale de novo peptide and miniprotein structure prediction.

Maupetit J, Derreumaux P, Tufféry P.

J Comput Chem. 2010 Mar;31(4):726-38. doi: 10.1002/jcc.21365.

PMID:
19569182
15.

MutDB services: interactive structural analysis of mutation data.

Dantzer J, Moad C, Heiland R, Mooney S.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W311-4.

16.
18.

Codep: maximizing co-evolutionary interdependencies to discover interacting proteins.

Tillier ER, Biro L, Li G, Tillo D.

Proteins. 2006 Jun 1;63(4):822-31.

PMID:
16634043
19.

An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D.

Izarzugaza JM, Baresic A, McMillan LE, Yeats C, Clegg AB, Orengo CA, Martin AC, Valencia A.

BMC Bioinformatics. 2009 Aug 27;10 Suppl 8:S5. doi: 10.1186/1471-2105-10-S8-S5.

20.

Effects of point mutations on protein structure are nonexponentially distributed.

Arodź T, Płonka PM.

Proteins. 2012 Jul;80(7):1780-90. doi: 10.1002/prot.24073.

PMID:
22434500

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