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Items: 1 to 20 of 155


bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming.

Gao J, Zhang Q, Liu M, Zhu L, Wu D, Cao Z, Zhu R.

J Cheminform. 2016 Jul 11;8:38. doi: 10.1186/s13321-016-0149-z. eCollection 2016.


Comparative Protein Structure Modeling Using MODELLER.

Webb B, Sali A.

Curr Protoc Bioinformatics. 2016 Jun 20;54:5.6.1-5.6.37. doi: 10.1002/cpbi.3.


Addressing the Role of Conformational Diversity in Protein Structure Prediction.

Palopoli N, Monzon AM, Parisi G, Fornasari MS.

PLoS One. 2016 May 9;11(5):e0154923. doi: 10.1371/journal.pone.0154923. eCollection 2016.


CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state.

Monzon AM, Rohr CO, Fornasari MS, Parisi G.

Database (Oxford). 2016 Mar 28;2016. pii: baw038. doi: 10.1093/database/baw038. Print 2016.



Rodriguez A, Schmidler SC.

Ann Appl Stat. 2014;8(4):2068-2095. Epub 2014 Dec 19.


Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner.

Gutiérrez FI, Rodriguez-Valenzuela F, Ibarra IL, Devos DP, Melo F.

BMC Bioinformatics. 2016 Jan 5;17:20. doi: 10.1186/s12859-015-0866-8.


A polynomial time algorithm for computing the area under a GDT curve.

Poleksic A.

Algorithms Mol Biol. 2015 Oct 26;10:27. doi: 10.1186/s13015-015-0058-0. eCollection 2015.


CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

Terashi G, Takeda-Shitaka M.

PLoS One. 2015 Oct 26;10(10):e0141440. doi: 10.1371/journal.pone.0141440. eCollection 2015.


Structural Bridges through Fold Space.

Edwards H, Deane CM.

PLoS Comput Biol. 2015 Sep 15;11(9):e1004466. doi: 10.1371/journal.pcbi.1004466. eCollection 2015 Sep.


Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding.

He L, Cheng Y, Kong L, Azadnia P, Giang E, Kim J, Wood MR, Wilson IA, Law M, Zhu J.

Sci Rep. 2015 Aug 4;5:12501. doi: 10.1038/srep12501.


STAR3D: a stack-based RNA 3D structural alignment tool.

Ge P, Zhang S.

Nucleic Acids Res. 2015 Nov 16;43(20):e137. doi: 10.1093/nar/gkv697. Epub 2015 Jul 15.


Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy.

Stamm M, Forrest LR.

Proteins. 2015 Sep;83(9):1720-32. doi: 10.1002/prot.24857. Epub 2015 Aug 1. Erratum in: Proteins. 2016 Sep;84(9):1333.


Finding optimal interaction interface alignments between biological complexes.

Cui X, Naveed H, Gao X.

Bioinformatics. 2015 Jun 15;31(12):i133-41. doi: 10.1093/bioinformatics/btv242.


Consistent global structures of complex RNA states through multidimensional chemical mapping.

Cheng CY, Chou FC, Kladwang W, Tian S, Cordero P, Das R.

Elife. 2015 Jun 2;4:e07600. doi: 10.7554/eLife.07600. Erratum in: Elife. 2015;4:e10095.


BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles.

Putnam DK, Weiner BE, Woetzel N, Lowe EW Jr, Meiler J.

Proteins. 2015 Aug;83(8):1500-12. doi: 10.1002/prot.24838. Epub 2015 Jul 1.


Computational tools for epitope vaccine design and evaluation.

He L, Zhu J.

Curr Opin Virol. 2015 Apr;11:103-12. doi: 10.1016/j.coviro.2015.03.013. Epub 2015 Mar 31. Review.


Ligand-target prediction by structural network biology using nAnnoLyze.

Martínez-Jiménez F, Marti-Renom MA.

PLoS Comput Biol. 2015 Mar 27;11(3):e1004157. doi: 10.1371/journal.pcbi.1004157. eCollection 2015 Mar.


Molecular dynamics study of naturally existing cavity couplings in proteins.

Barbany M, Meyer T, Hospital A, Faustino I, D'Abramo M, Morata J, Orozco M, de la Cruz X.

PLoS One. 2015 Mar 27;10(3):e0119978. doi: 10.1371/journal.pone.0119978. eCollection 2015.


Analysis of nidogen-1/laminin γ1 interaction by cross-linking, mass spectrometry, and computational modeling reveals multiple binding modes.

Lössl P, Kölbel K, Tänzler D, Nannemann D, Ihling CH, Keller MV, Schneider M, Zaucke F, Meiler J, Sinz A.

PLoS One. 2014 Nov 11;9(11):e112886. doi: 10.1371/journal.pone.0112886. eCollection 2014.


Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator.

Chakraborty S, Rao BJ, Baker N, Asgeirsson B.

Intrinsically Disord Proteins. 2013;1. pii: e25463.

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