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Items: 1 to 20 of 118


Modeling Electrostatic Force in Protein-Protein Recognition.

Shashikala HBM, Chakravorty A, Alexov E.

Front Mol Biosci. 2019 Sep 25;6:94. doi: 10.3389/fmolb.2019.00094. eCollection 2019.


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.


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.


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.


A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.

Hazra T, Ahmed Ullah S, Wang S, Alexov E, Zhao S.

J Math Biol. 2019 Jul;79(2):631-672. doi: 10.1007/s00285-019-01372-1. Epub 2019 Apr 27.


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.


Processivity vs. Beating: Comparing Cytoplasmic and Axonemal Dynein Microtubule Binding Domain Association with Microtubule.

Tajielyato N, Alexov E.

Int J Mol Sci. 2019 Mar 3;20(5). pii: E1090. doi: 10.3390/ijms20051090.


PKAD: a database of experimentally measured pKa values of ionizable groups in proteins.

Pahari S, Sun L, Alexov E.

Database (Oxford). 2019 Jan 1;2019. pii: baz024. doi: 10.1093/database/baz024.


A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry.

Chakravorty A, Gallicchio E, Alexov E.

J Comput Chem. 2019 May 5;40(12):1290-1304. doi: 10.1002/jcc.25786. Epub 2019 Jan 30.


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.


DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate.

Pahari S, Sun L, Basu S, Alexov E.

Proteins. 2018 Dec;86(12):1277-1283. doi: 10.1002/prot.25608. Epub 2018 Oct 26.


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.


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.


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.


Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.

Chakravorty A, Jia Z, Li L, Zhao S, Alexov E.

J Chem Theory Comput. 2018 Feb 13;14(2):1020-1032. doi: 10.1021/acs.jctc.7b00756. Epub 2018 Feb 3.


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.


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.


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.


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.

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