Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 89

1.

Protein signatures using electrostatic molecular surfaces in harmonic space.

Carvalho CS, Vlachakis D, Tsiliki G, Megalooikonomou V, Kossida S.

PeerJ. 2013 Oct 22;1:e185. doi: 10.7717/peerj.185. eCollection 2013.

PMID:
24167780
[PubMed]
Free PMC Article
2.

On the difference in quality between current heuristic and optimal solutions to the protein structure alignment problem.

Arriagada M, Poleksic A.

Biomed Res Int. 2013;2013:459248. doi: 10.1155/2013/459248. Epub 2012 Dec 23.

PMID:
23509725
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Toward a "structural BLAST": using structural relationships to infer function.

Dey F, Cliff Zhang Q, Petrey D, Honig B.

Protein Sci. 2013 Apr;22(4):359-66. doi: 10.1002/pro.2225. Epub 2013 Feb 21. Review.

PMID:
23349097
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

The difficulty of protein structure alignment under the RMSD.

Li SC.

Algorithms Mol Biol. 2013 Jan 4;8(1):1. doi: 10.1186/1748-7188-8-1.

PMID:
23286762
[PubMed]
Free PMC Article
5.

Benefits of using molecular structure and abundance in phylogenomic analysis.

Caetano-Anoll├ęs G, Nasir A.

Front Genet. 2012 Sep 6;3:172. doi: 10.3389/fgene.2012.00172. eCollection 2012. No abstract available.

PMID:
22973296
[PubMed]
Free PMC Article
6.

How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis.

Vihinen M.

BMC Genomics. 2012 Jun 18;13 Suppl 4:S2. doi: 10.1186/1471-2164-13-S4-S2.

PMID:
22759650
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Overcoming sequence misalignments with weighted structural superposition.

Khazanov NA, Damm-Ganamet KL, Quang DX, Carlson HA.

Proteins. 2012 Nov;80(11):2523-35. doi: 10.1002/prot.24134. Epub 2012 Jul 28.

PMID:
22733542
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
9.

A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction.

Yang Y, Zhan J, Zhao H, Zhou Y.

Proteins. 2012 Aug;80(8):2080-8. doi: 10.1002/prot.24100. Epub 2012 May 25.

PMID:
22522696
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Evolutionary inaccuracy of pairwise structural alignments.

Sadowski MI, Taylor WR.

Bioinformatics. 2012 May 1;28(9):1209-15. doi: 10.1093/bioinformatics/bts103. Epub 2012 Mar 6.

PMID:
22399676
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns.

Pires DE, de Melo-Minardi RC, dos Santos MA, da Silveira CH, Santoro MM, Meira W Jr.

BMC Genomics. 2011 Dec 22;12 Suppl 4:S12. doi: 10.1186/1471-2164-12-S4-S12. Epub 2011 Dec 22.

PMID:
22369665
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Accelerating large-scale protein structure alignments with graphics processing units.

Pang B, Zhao N, Becchi M, Korkin D, Shyu CR.

BMC Res Notes. 2012 Feb 22;5:116. doi: 10.1186/1756-0500-5-116.

PMID:
22357132
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison.

Razmara J, Deris S, Parvizpour S.

Algorithms Mol Biol. 2012 Feb 15;7:4. doi: 10.1186/1748-7188-7-4.

PMID:
22336468
[PubMed]
Free PMC Article
14.

IndelFR: a database of indels in protein structures and their flanking regions.

Zhang Z, Xing C, Wang L, Gong B, Liu H.

Nucleic Acids Res. 2012 Jan;40(Database issue):D512-8. doi: 10.1093/nar/gkr1107. Epub 2011 Nov 29.

PMID:
22127860
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A novel method to compare protein structures using local descriptors.

Daniluk P, Lesyng B.

BMC Bioinformatics. 2011 Aug 17;12:344. doi: 10.1186/1471-2105-12-344.

PMID:
21849047
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

The significance of the ProtDeform score for structure prediction and alignment.

Rocha J, Alberich R.

PLoS One. 2011;6(6):e20889. doi: 10.1371/journal.pone.0020889. Epub 2011 Jun 28.

PMID:
21738592
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Maps of protein structure space reveal a fundamental relationship between protein structure and function.

Osadchy M, Kolodny R.

Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12301-6. doi: 10.1073/pnas.1102727108. Epub 2011 Jul 7.

PMID:
21737750
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Multi-view methods for protein structure comparison using latent dirichlet allocation.

Shivashankar S, Srivathsan S, Ravindran B, Tendulkar AV.

Bioinformatics. 2011 Jul 1;27(13):i61-8. doi: 10.1093/bioinformatics/btr249.

PMID:
21685102
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

MarkUs: a server to navigate sequence-structure-function space.

Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W357-61. doi: 10.1093/nar/gkr468. Epub 2011 Jun 14.

PMID:
21672961
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

R3D-BLAST: a search tool for similar RNA 3D substructures.

Liu YC, Yang CH, Chen KT, Wang JR, Cheng ML, Chung JC, Chiu HT, Lu CL.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W45-9. doi: 10.1093/nar/gkr379. Epub 2011 May 29.

PMID:
21624889
[PubMed - indexed for MEDLINE]
Free PMC Article

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Write to the Help Desk