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Results: 1 to 20 of 131

1.

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.

PMID:
25387007
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
25364645
[PubMed]
Free PMC Article
3.

A method of protein model classification and retrieval using bag-of-visual-features.

Ma J, Ma Z, Kang B, Lu K.

Comput Math Methods Med. 2014;2014:269394. doi: 10.1155/2014/269394. Epub 2014 Sep 1.

PMID:
25258644
[PubMed - in process]
Free PMC Article
4.

Conformation-independent structural comparison of macromolecules with ProSMART.

Nicholls RA, Fischer M, McNicholas S, Murshudov GN.

Acta Crystallogr D Biol Crystallogr. 2014 Sep;70(Pt 9):2487-99. doi: 10.1107/S1399004714016241. Epub 2014 Aug 29.

PMID:
25195761
[PubMed - in process]
Free PMC Article
5.

Identifying druggable targets by protein microenvironments matching: application to transcription factors.

Liu T, Altman RB.

CPT Pharmacometrics Syst Pharmacol. 2014 Jan 22;3:e93. doi: 10.1038/psp.2013.66.

PMID:
24452614
[PubMed]
Free PMC Article
6.

BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry.

Rueda M, Orozco M, Totrov M, Abagyan R.

BMC Struct Biol. 2013 Dec 13;13:32. doi: 10.1186/1472-6807-13-32.

PMID:
24330655
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Structure and stability insights into tumour suppressor p53 evolutionary related proteins.

Pagano B, Jama A, Martinez P, Akanho E, Bui TT, Drake AF, Fraternali F, Nikolova PV.

PLoS One. 2013 Oct 4;8(10):e76014. doi: 10.1371/journal.pone.0076014. eCollection 2013.

PMID:
24124530
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Definition and classification of evaluation units for CASP10.

Taylor TJ, Tai CH, Huang YJ, Block J, Bai H, Kryshtafovych A, Montelione GT, Lee B.

Proteins. 2014 Feb;82 Suppl 2:14-25. doi: 10.1002/prot.24434. Epub 2013 Nov 22.

PMID:
24123179
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.

Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA.

PLoS Comput Biol. 2013;9(10):e1003253. doi: 10.1371/journal.pcbi.1003253. Epub 2013 Oct 3.

PMID:
24098102
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures.

Brylinski M.

BMC Res Notes. 2013 Jul 31;6:303. doi: 10.1186/1756-0500-6-303.

PMID:
23902875
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling.

Macdonald JT, Kelley LA, Freemont PS.

PLoS One. 2013 Jun 18;8(6):e65770. Print 2013.

PMID:
23824634
[PubMed - as supplied by publisher]
Free PMC Article
12.

A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases.

López-Pelegrín M, Cerdà-Costa N, Martínez-Jiménez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA, López-Otín C, Arolas JL, Gomis-Rüth FX.

J Biol Chem. 2013 Jul 19;288(29):21279-94. doi: 10.1074/jbc.M113.476580. Epub 2013 Jun 3.

PMID:
23733187
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Learning a peptide-protein binding affinity predictor with kernel ridge regression.

Giguère S, Marchand M, Laviolette F, Drouin A, Corbeil J.

BMC Bioinformatics. 2013 Mar 5;14:82. doi: 10.1186/1471-2105-14-82.

PMID:
23497081
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The twilight zone of cis element alignments.

Sebastian A, Contreras-Moreira B.

Nucleic Acids Res. 2013 Feb 1;41(3):1438-49. doi: 10.1093/nar/gks1301. Epub 2012 Dec 24.

PMID:
23268451
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Evolutionary dynamics on protein bi-stability landscapes can potentially resolve adaptive conflicts.

Sikosek T, Bornberg-Bauer E, Chan HS.

PLoS Comput Biol. 2012;8(9):e1002659. doi: 10.1371/journal.pcbi.1002659. Epub 2012 Sep 13.

PMID:
23028272
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

A comparison of genotype-phenotype maps for RNA and proteins.

Ferrada E, Wagner A.

Biophys J. 2012 Apr 18;102(8):1916-25. doi: 10.1016/j.bpj.2012.01.047.

PMID:
22768948
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Patterns of evolutionary conservation of essential genes correlate with their compensability.

Bergmiller T, Ackermann M, Silander OK.

PLoS Genet. 2012 Jun;8(6):e1002803. doi: 10.1371/journal.pgen.1002803. Epub 2012 Jun 28.

PMID:
22761596
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions.

Juritz E, Fornasari MS, Martelli PL, Fariselli P, Casadio R, Parisi G.

BMC Genomics. 2012 Jun 18;13 Suppl 4:S5. doi: 10.1186/1471-2164-13-S4-S5.

PMID:
22759653
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Crystal structure of the catalytic domain of the Bacillus cereus SleB protein, important in cortex peptidoglycan degradation during spore germination.

Li Y, Jin K, Setlow B, Setlow P, Hao B.

J Bacteriol. 2012 Sep;194(17):4537-45. doi: 10.1128/JB.00877-12. Epub 2012 Jun 22.

PMID:
22730118
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

SAS-Pro: simultaneous residue assignment and structure superposition for protein structure alignment.

Shah SB, Sahinidis NV.

PLoS One. 2012;7(5):e37493. doi: 10.1371/journal.pone.0037493. Epub 2012 May 25.

PMID:
22662161
[PubMed - indexed for MEDLINE]
Free PMC Article

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