Recent Publications

See Dr. Wei's site for more publications

Nguyen DD, Wei GW. “AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening.” J Chem Inf Model. (2019) Jul 1. doi: 10.1021/acs.jcim.9b00334

Nguyen DD, Wei GW. “DG-GL: Differential geometry based geometric learning of molecular datasets.” Int J Numer Method Biomed Eng. (2019) Jan 28;e3179. doi: 10.1002/cnm.3179

Zhao R, Cang Z, Tong Y, Wei GW. “Protein pocket detection via convex hull surface evolution and associated Reeb graph.” Bioinformatics. (2018) Sep 1;34(17):i830-i837. doi: 10.1093/bioinformatics/bty598

Bramer D, Wei GW. “Blind prediction of protein B-factor and flexibility.” J Chem Phys. (2018) Oct 7;149(13):134107. doi: 10.1063/1.5048469

Nguyen DD, Cang Z, Wu K, Wang M, Cao Y, Wei GW. “Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges.” J Comput Aided Mol Des. (2018) Aug 16. doi: 10.1007/s10822-018-0146-6

Wu K, Zhao Z, Wang R, Wei GW. “TopP-S: Persistent homology-based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility.” J Comput Chem. (2018) Apr 6. doi: 10.1002/jcc.25213

Bramer D, Wei GW. “Multiscale weighted colored graphs for protein flexibility and rigidity analysis.” J Chem Phys. (2018) Feb 7;148(5):054103. doi: 10.1063/1.5016562

Wu K, Wei GW. “Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks.” J Chem Inf Model. (2018) Jan 31. doi: 10.1021/acs.jcim.7b00558

Cang Z, Mu L, Wei GW. “Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening.” PLoS Comput Biol. (2018) Jan 8;14(1):e1005929. doi: 10.1371/journal.pcbi.1005929

Cang Z, Wei GW. “Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology.” Bioinformatics. (2017) Nov 15;33(22):3549-3557. doi: 10.1093/bioinformatics/btx460

Wang B, Wang C, Wu K, Wei GW. “Breaking the polar-nonpolar division in solvation free energy prediction.” J Comput Chem. (2017) Nov 11. doi: 10.1002/jcc.25107

Nedialkov YA, Opron K, Caudill HL, Assaf F, Anderson AJ, Cukier RI, Wei G, Burton ZF. “Hinge action versus grip in translocation by RNA polymerase.” Transcription. (2017) Aug 30;e1330179. doi: 10.1080/21541264.2017.1330179

Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. “Improvements to the APBS biomolecular solvation software suite.” Protein Sci. (2017) Aug 24;. doi: 10.1002/pro.3280

Cang Z, Wei GW. “TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions.” PLoS Comput Biol. (2017) Jul 27;13(7):e1005690. doi: 10.1371/journal.pcbi.1005690

Nguyen DD, Xiao T, Wang M, Wei GW. “Rigidity Strengthening: A Mechanism for Protein-Ligand Binding.” J Chem Inf Model. (2017) Jul 24;57(7):1715-1721. doi: 10.1021/acs.jcim.7b00226

Cang Z, Wei GW. “Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology.” Bioinformatics. (2017) Jul 14. doi: 10.1093/bioinformatics/btx460

Cang Z, Wei GW. “Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction.” Int J Numer Method Biomed Eng. (2017) Jul 5. doi: 10.1002/cnm.2914

Nguyen DD, Wang B, Wei GW. “Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies.” J Comput Chem. (2017) Feb 16. doi: 10.1002/jcc.24757

Liu B, Wang B, Zhao R, Tong Y, Wei GW. “ESES: Software for Eulerian solvent excluded surface.” J Comput Chem. (2017) Jan 4. doi: 10.1002/jcc.24682

Nguyen DD, Wei GW. “The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling.” J Comput Chem. (2016) Oct 8. doi: 10.1002/jcc.24512

Wang B, Zhao Z, Wei GW. “Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies.” J Chem Phys. (2016) Sep 28;145(12):124110. doi: 10.1063/1.4963193

Nguyen DD, Xia K, Wei GW. “Generalized flexibility-rigidity index.” J Chem Phys. (2016) Jun 21;144(23):234106. doi:10.1063/1.4953851

Opron K, Xia K, Burton Z, Wei GW. “Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.” J Comput Chem. (2016) May 30;37(14):1283-95. doi:10.1002/jcc.24320

Wang B, Wei GW. “Object-oriented Persistent Homology.” J Comput Phys. (2016) Jan 15;305:276-299. doi:10.1016/j.jcp.2015.10.036

Xia K, Feng X, Chen Z, Tong Y, Wei GW. "Multiscale geometric modeling of macromolecules I: Cartesian representation." J Comput Phys. (2014) doi:10.1016/j.jcp.2013.09.034.

Hu L, Chen D, Wei GW. “High-order fractional partial differential equation transform for molecular surface construction.” Molecular Based Mathematical Biology 1 (2012): 1-25. 2 doi:10.2478/mlbmb-2012-0001.

Xia K, Opron K, Wei GW. "Multiscale multiphysics and multidomain models-Flexibility and rigidity." J Chem Phys. (2013) doi:10.1063/1.4830404.

Feng X, Xia K, Chen Z, Tong Y, Wei GW. “Multiscale geometric modeling of macromolecules II: Lagrangian representation.” Journal of Computational Chemistry 34.24 (2013): 2100-20. doi:10.1002/jcc.v34.24.

Park J, Wei GW. “A molecular level prototype for mechanoelectrical transducer in mammalian hair cells.” Journal of Computational Neuroscience 35.2 (2013): 231-41. doi:10.1007/s10827-013-0450-z.

Chen D, Wei GW. "Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation." Commun Comput Phys. (2013) doi:10.4208/cicp.050511.050811s.

Feng X, Xia K, Tong Y, Wei GW. “Geometric modeling of subcellular structures, organelles, and multiprotein complexes.” International Journal for Numerical Methods in Biomedical Engineering 28.12 (2012): 1198-23. doi:10.1002/cnm.v28.12.

Wei GW, Zheng Q, Chen Z, Xia K. “Variational Multiscale Models for Charge Transport.” SIAM Review 54.4 (2012): 699-754. doi:10.1137/110845690.

Hu L, Wei GW. “Nonlinear Poisson Equation for Heterogeneous Media.” Biophysical Journal 103.4 (2012): 758-66. doi:10.1016/j.bpj.2012.07.006.