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Items: 24

1.

A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.

Kimchi O, Cragnolini T, Brenner MP, Colwell LJ.

Biophys J. 2019 Aug 6;117(3):520-532. doi: 10.1016/j.bpj.2019.06.037. Epub 2019 Jul 10.

PMID:
31353036
2.

Using attribution to decode binding mechanism in neural network models for chemistry.

McCloskey K, Taly A, Monti F, Brenner MP, Colwell LJ.

Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11624-11629. doi: 10.1073/pnas.1820657116. Epub 2019 May 24.

PMID:
31127041
3.

Proline provides site-specific flexibility for in vivo collagen.

Chow WY, Forman CJ, Bihan D, Puszkarska AM, Rajan R, Reid DG, Slatter DA, Colwell LJ, Wales DJ, Farndale RW, Duer MJ.

Sci Rep. 2018 Sep 14;8(1):13809. doi: 10.1038/s41598-018-31937-x.

4.

Analysis of nanobody paratopes reveals greater diversity than classical antibodies.

Mitchell LS, Colwell LJ.

Protein Eng Des Sel. 2018 Jul 1;31(7-8):267-275. doi: 10.1093/protein/gzy017.

5.

Comparative analysis of nanobody sequence and structure data.

Mitchell LS, Colwell LJ.

Proteins. 2018 Jul;86(7):697-706. doi: 10.1002/prot.25497. Epub 2018 Apr 15.

6.

Statistical and machine learning approaches to predicting protein-ligand interactions.

Colwell LJ.

Curr Opin Struct Biol. 2018 Apr;49:123-128. doi: 10.1016/j.sbi.2018.01.006. Epub 2018 Feb 20. Review.

PMID:
29452923
7.

Power law tails in phylogenetic systems.

Qin C, Colwell LJ.

Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):690-695. doi: 10.1073/pnas.1711913115. Epub 2018 Jan 8.

8.

Optimal Design of Experiments by Combining Coarse and Fine Measurements.

Lee AA, Brenner MP, Colwell LJ.

Phys Rev Lett. 2017 Nov 17;119(20):208101. doi: 10.1103/PhysRevLett.119.208101. Epub 2017 Nov 16.

PMID:
29219382
9.

Predicting protein-ligand affinity with a random matrix framework.

Lee AA, Brenner MP, Colwell LJ.

Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):13564-13569. Epub 2016 Nov 16.

10.

Inferring interaction partners from protein sequences.

Bitbol AF, Dwyer RS, Colwell LJ, Wingreen NS.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12180-12185. Epub 2016 Sep 23.

11.

The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein.

Townsend PD, Rodgers TL, Glover LC, Korhonen HJ, Richards SA, Colwell LJ, Pohl E, Wilson MR, Hodgson DR, McLeish TC, Cann MJ.

J Biol Chem. 2015 Sep 4;290(36):22225-35. doi: 10.1074/jbc.M115.669267. Epub 2015 Jul 16.

12.

Protein sectors: statistical coupling analysis versus conservation.

Teşileanu T, Colwell LJ, Leibler S.

PLoS Comput Biol. 2015 Feb 27;11(2):e1004091. doi: 10.1371/journal.pcbi.1004091. eCollection 2015 Feb.

13.

Conservation weighting functions enable covariance analyses to detect functionally important amino acids.

Colwell LJ, Brenner MP, Murray AW.

PLoS One. 2014 Nov 7;9(11):e107723. doi: 10.1371/journal.pone.0107723. eCollection 2014.

14.

Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis.

Dwyer RS, Ricci DP, Colwell LJ, Silhavy TJ, Wingreen NS.

Genetics. 2013 Oct;195(2):443-55. doi: 10.1534/genetics.113.155861. Epub 2013 Aug 9.

15.

The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture.

Perica T, Marsh JA, Sousa FL, Natan E, Colwell LJ, Ahnert SE, Teichmann SA.

Biochem Soc Trans. 2012 Jun 1;40(3):475-91. doi: 10.1042/BST20120056.

PMID:
22616857
16.

Three-dimensional structures of membrane proteins from genomic sequencing.

Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS.

Cell. 2012 Jun 22;149(7):1607-21. doi: 10.1016/j.cell.2012.04.012. Epub 2012 May 10.

17.

The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.

18.

A core subunit of Polycomb repressive complex 1 is broadly conserved in function but not primary sequence.

Beh LY, Colwell LJ, Francis NJ.

Proc Natl Acad Sci U S A. 2012 May 1;109(18):E1063-71. doi: 10.1073/pnas.1118678109. Epub 2012 Apr 18.

19.

Protein 3D structure computed from evolutionary sequence variation.

Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C.

PLoS One. 2011;6(12):e28766. doi: 10.1371/journal.pone.0028766. Epub 2011 Dec 7.

20.

Charge as a selection criterion for translocation through the nuclear pore complex.

Colwell LJ, Brenner MP, Ribbeck K.

PLoS Comput Biol. 2010 Apr 22;6(4):e1000747. doi: 10.1371/journal.pcbi.1000747.

21.

Action potential initiation in the hodgkin-huxley model.

Colwell LJ, Brenner MP.

PLoS Comput Biol. 2009 Jan;5(1):e1000265. doi: 10.1371/journal.pcbi.1000265. Epub 2009 Jan 16.

22.

Effects of an irritable bowel syndrome educational class on health-promoting behaviors and symptoms.

Colwell LJ, Prather CM, Phillips SF, Zinsmeister AR.

Am J Gastroenterol. 1998 Jun;93(6):901-5.

PMID:
9647015
23.

Achalasia: prospective evaluation of relationship between lower esophageal sphincter pressure, esophageal transit, and esophageal diameter and symptoms in response to pneumatic dilation.

Kim CH, Cameron AJ, Hsu JJ, Talley NJ, Trastek VF, Pairolero PC, O'Connor MK, Colwell LJ, Zinsmeister AR.

Mayo Clin Proc. 1993 Nov;68(11):1067-73.

PMID:
8231271
24.

The combination of prednisone and colchicine in patients with primary sclerosing cholangitis.

Lindor KD, Wiesner RH, Colwell LJ, Steiner B, Beaver S, LaRusso NF.

Am J Gastroenterol. 1991 Jan;86(1):57-61.

PMID:
1986556

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