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Items: 1 to 20 of 87

1.

Exploring the nonlinear geometry of protein homology.

Farnum MA, Xu H, Agrafiotis DK.

Protein Sci. 2003 Aug;12(8):1604-12.

2.

A geodesic framework for analyzing molecular similarities.

Agrafiotis DK, Xu H.

J Chem Inf Comput Sci. 2003 Mar-Apr;43(2):475-84.

PMID:
12653511
3.

Automatic classification of protein structures using low-dimensional structure space mappings.

Asarnow D, Singh R.

BMC Bioinformatics. 2014;15 Suppl 2:S1. doi: 10.1186/1471-2105-15-S2-S1. Epub 2014 Jan 24.

4.

Stochastic proximity embedding.

Agrafiotis DK.

J Comput Chem. 2003 Jul 30;24(10):1215-21.

PMID:
12820129
5.

A modified update rule for stochastic proximity embedding.

Rassokhin DN, Agrafiotis DK.

J Mol Graph Model. 2003 Nov;22(2):133-40.

PMID:
12932784
6.

Incorporating homologues into sequence embeddings for protein analysis.

Eskin E, Snir S.

J Bioinform Comput Biol. 2007 Jun;5(3):717-38.

PMID:
17688313
7.

Multidimensional scaling for large genomic data sets.

Tzeng J, Lu HH, Li WH.

BMC Bioinformatics. 2008 Apr 4;9:179. doi: 10.1186/1471-2105-9-179.

8.

Detecting remote evolutionary relationships among proteins by large-scale semantic embedding.

Melvin I, Weston J, Noble WS, Leslie C.

PLoS Comput Biol. 2011 Jan 27;7(1):e1001047. doi: 10.1371/journal.pcbi.1001047.

9.

A new seed selection algorithm that maximizes local structural similarity in proteins.

Altun G, Zhong W, Pan Y, Tai PC, Harrison RW.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:5822-5.

PMID:
17946336
10.

A self-organizing principle for learning nonlinear manifolds.

Agrafiotis DK, Xu H.

Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15869-72. Epub 2002 Nov 20.

11.

Computing energy landscape maps and structural excursions of proteins.

Sapin E, Carr DB, De Jong KA, Shehu A.

BMC Genomics. 2016 Aug 18;17 Suppl 4:546. doi: 10.1186/s12864-016-2798-8.

12.

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.

Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A.

PLoS Comput Biol. 2009 Jan;5(1):e1000267. doi: 10.1371/journal.pcbi.1000267. Epub 2009 Jan 23.

13.

Application of Kohonen maps for solving the classification puzzle in AGC kinase protein sequences.

Murty US, Banerjee AK, Arora N.

Interdiscip Sci. 2009 Sep;1(3):173-8. doi: 10.1007/s12539-009-0032-1. Epub 2009 Aug 7.

PMID:
20640835
14.

BioGPS: navigating biological space to predict polypharmacology, off-targeting, and selectivity.

Siragusa L, Cross S, Baroni M, Goracci L, Cruciani G.

Proteins. 2015 Mar;83(3):517-32. doi: 10.1002/prot.24753. Epub 2015 Jan 24.

15.

A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes.

Clausen R, Shehu A.

J Comput Biol. 2015 Sep;22(9):844-60. doi: 10.1089/cmb.2015.0107. Epub 2015 Jul 23.

PMID:
26203626
16.

Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property.

Zhong W, Altun G, Harrison R, Tai PC, Pan Y.

IEEE Trans Nanobioscience. 2005 Sep;4(3):255-65.

PMID:
16220690
17.

Surface-based protein binding pocket similarity.

Spitzer R, Cleves AE, Jain AN.

Proteins. 2011 Sep;79(9):2746-63. doi: 10.1002/prot.23103. Epub 2011 Jul 18.

18.

Stochastic proximity embedding on graphics processing units: taking multidimensional scaling to a new scale.

Yang E, Liu P, Rassokhin DN, Agrafiotis DK.

J Chem Inf Model. 2011 Nov 28;51(11):2852-9. doi: 10.1021/ci200420c. Epub 2011 Oct 21.

PMID:
21961974
19.

A surface of minimum area metric for the structural comparison of proteins.

Falicov A, Cohen FE.

J Mol Biol. 1996 May 24;258(5):871-92.

PMID:
8637017
20.

A map of the protein space--an automatic hierarchical classification of all protein sequences.

Yona G, Linial N, Tishby N, Linial M.

Proc Int Conf Intell Syst Mol Biol. 1998;6:212-21.

PMID:
9783227

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