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Items: 18

1.

Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women.

Wu B, Peng Y, Eggert J, Alexov E.

Int J Mol Sci. 2019 Sep 28;20(19). pii: E4828. doi: 10.3390/ijms20194828.

2.

DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor: Application to Spermine Synthase Enzyme.

Peng Y, Yang Y, Li L, Jia Z, Cao W, Alexov E.

Front Mol Biosci. 2019 Sep 4;6:74. doi: 10.3389/fmolb.2019.00074. eCollection 2019. Erratum in: Front Mol Biosci. 2019 Oct 29;6:111.

3.

DelPhi Suite: New Developments and Review of Functionalities.

Li C, Jia Z, Chakravorty A, Pahari S, Peng Y, Basu S, Koirala M, Panday SK, Petukh M, Li L, Alexov E.

J Comput Chem. 2019 Oct 30;40(28):2502-2508. doi: 10.1002/jcc.26006. Epub 2019 Jun 25.

4.

Three additional patients with EED-associated overgrowth: potential mutation hotspots identified?

Spellicy CJ, Peng Y, Olewiler L, Cathey SS, Rogers RC, Bartholomew D, Johnson J, Alexov E, Lee JA, Friez MJ, Jones JR.

J Hum Genet. 2019 Jun;64(6):561-572. doi: 10.1038/s10038-019-0585-5. Epub 2019 Mar 11.

PMID:
30858506
5.

Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases.

Peng Y, Alexov E, Basu S.

Int J Mol Sci. 2019 Jan 28;20(3). pii: E548. doi: 10.3390/ijms20030548. Review.

6.

E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein.

Tajielyato N, Li L, Peng Y, Alper J, Alexov E.

Sci Rep. 2018 Sep 5;8(1):13266. doi: 10.1038/s41598-018-31480-9.

7.

Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents.

Chakravorty A, Jia Z, Peng Y, Tajielyato N, Wang L, Alexov E.

Front Mol Biosci. 2018 Mar 27;5:25. doi: 10.3389/fmolb.2018.00025. eCollection 2018.

8.

Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects.

Spellicy CJ, Norris J, Bend R, Bupp C, Mester P, Reynolds T, Dean J, Peng Y, Alexov E, Schwartz CE, Stevenson RS, J Friez M.

Eur J Hum Genet. 2018 Mar;26(3):420-427. doi: 10.1038/s41431-017-0025-y. Epub 2018 Jan 22.

9.

Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith-Lemli-Opitz Syndrome.

Peng Y, Myers R, Zhang W, Alexov E.

Int J Mol Sci. 2018 Jan 4;19(1). pii: E141. doi: 10.3390/ijms19010141.

10.

Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.

Peng Y, Sun L, Jia Z, Li L, Alexov E.

Bioinformatics. 2018 Mar 1;34(5):779-786. doi: 10.1093/bioinformatics/btx698.

11.

DelPhiForce web server: electrostatic forces and energy calculations and visualization.

Li L, Jia Z, Peng Y, Chakravorty A, Sun L, Alexov E.

Bioinformatics. 2017 Nov 15;33(22):3661-3663. doi: 10.1093/bioinformatics/btx495.

12.

Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations.

Li L, Jia Z, Peng Y, Godar S, Getov I, Teng S, Alper J, Alexov E.

Sci Rep. 2017 Aug 15;7(1):8237. doi: 10.1038/s41598-017-08419-7.

13.

Identification and characterization of a missense mutation in the O-linked β-N-acetylglucosamine (O-GlcNAc) transferase gene that segregates with X-linked intellectual disability.

Vaidyanathan K, Niranjan T, Selvan N, Teo CF, May M, Patel S, Weatherly B, Skinner C, Opitz J, Carey J, Viskochil D, Gecz J, Shaw M, Peng Y, Alexov E, Wang T, Schwartz C, Wells L.

J Biol Chem. 2017 May 26;292(21):8948-8963. doi: 10.1074/jbc.M116.771030. Epub 2017 Mar 16.

14.

Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes.

Peng Y, Alexov E.

Proteins. 2017 Feb;85(2):282-295. doi: 10.1002/prot.25221. Epub 2017 Jan 5.

PMID:
27936518
15.

Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model.

Peng Y, Alexov E.

Proteins. 2016 Dec;84(12):1797-1809. doi: 10.1002/prot.25162. Epub 2016 Oct 1.

16.

Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase.

Peng Y, Norris J, Schwartz C, Alexov E.

Int J Mol Sci. 2016 Jan 8;17(1). pii: E77. doi: 10.3390/ijms17010077.

17.

Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding.

Peng Y, Alexov E.

Proteins. 2016 Feb;84(2):232-9. doi: 10.1002/prot.24968. Epub 2016 Jan 11.

18.

Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease.

Peng Y, Suryadi J, Yang Y, Kucukkal TG, Cao W, Alexov E.

Int J Mol Sci. 2015 Nov 13;16(11):27270-87. doi: 10.3390/ijms161126022.

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