PUBLICATIONS

I. Wichka and P.K. Lai*, “Rapid discovery of Transglutaminase 2 inhibitors for celiac disease with boosting ensemble machine learning”, Comput. Struct. Biotechnol. J., 23:3669–3679, 2024.

M.C. Harrison and P.K. Lai*, Investigating the mechanisms of antibody binding to alpha-synuclein for the treatment of Parkinson’s Disease, Mol. Pharm., 21:5326-5334, 2024. 

L. Kalejaye, I.E. Wu, T. Terry and P.K. Lai*, DeepSP: Deep Learning-Based Spatial Properties to Predict Monoclonal Antibody Stability, Comput. Struct. Biotechnol. J., 23:2220–2229, 2024.

A. Phillips, A. Srinivas, I. Prentoska, M. O'Dea, M. Kustrup, S. Hurley, S. Bruno, V. Nguyen and P.K. Lai*, Teaching biologics design using molecular modeling and simulations, Biochem Mol Biol Educ. 2024.

P.K. Lai*, DeepSCM: An efficient convolutional neural network surrogate model for the screening of therapeutic antibody viscosity, Comput. Struct. Biotechnol. J., 20:2143-2152, 2022.

P.K. Lai, A. Gallegos, N. Mody, H. A. Sathish, and B.L. Trout, Machine learning prediction of antibody aggregation and viscosity for high concentration formulation development of protein therapeutics", mAbs, 14(1):e2026208, 2022.

P.K. Lai#, G. Ghag#, Y. Yu#, V. Juan, L. Fayadat-Dilman and B.L. Trout, Differences in human IgG1 and IgG4 S228P monoclonal antibodies viscosity and self-interactions: Experimental assessment and computational predictions of domain interactions", mAbs, 13(1):e1991256, 2021.

P.K. Lai, J.W. Swan and B.L. Trout, Calculation of Therapeutic Antibody Viscosity with Coarse-Grained Models, Hydrodynamic Calculations and Machine-Learning-Based Parameters, mAbs, 13(1):e1907882, 2021.

P.K. Lai, A. Fernando, T.K. Cloutier, Y. Gokarn, J. Zhang, W. Schwenger, R. Chari, K.T. Halloran, C.C. Rubio and B.L. Trout, Machine Learning Applied to Determine the Molecular Descriptors Responsible for the Viscosity Behavior of Concentrated Therapeutic Antibodies, Mol. Pharm., 18(3):1167-1175, 2021.

P.K. Lai, A. Fernando, T.K. Cloutier, J.S. Kingsbury, Y. Gokarn, K.T. Halloran, C.C. Rubio and B.L. Trout, Machine Learning Feature Selection for Predicting High Concentration Therapeutic Antibody Aggregation, J. Pharm. Sci., 110(4):1583-1591, 2020

P.K. Lai, D.T. Tresnak and B. J. Hackel, Identication and Elucidation of Proline-rich Antimicrobial Peptides with Enhanced Potency and Delivery, Biotechnol Bioeng., 116:2439-2450, 2019.

P.K. Lai, K. Geldart, S. Ritter, Y.N. Kaznessis, and B.J. Hackel, Systematic Mutagenesis of Oncocin Reveals Enhanced Activity and Insights into the Mechanisms of Antimicrobial Activity, Mol. Syst. Des. Eng., 3:930-941, 2018.

P.K. Lai and Y.N. Kaznessis, Insights into Membrane Translocation of Protegrin Antimicrobial Peptides by Multistep Molecular Dynamics Simulations, ACS Omega,3(6):6056-6065, 2018.

P.K. Lai and Y.N. Kaznessis, Free Energy Calculations of Microcin J25 Variants Binding to the FhuA Receptor, J. Chem. Theory Comput., 13(7):3413-3423, 2017.

P.K. Lai and S.T. Lin, Internal Coordinate Density of State from Molecular Dynamics Simulation, J. Comput. Chem., 36(8):507-517, 2015.

P.K. Lai and S.T. Lin, Rapid Determination of Internal Rotation Entropy from the Two-Phase Thermodynamic Model, RSC Adv., 4(19):9522-9533, 2014.

A. Grunberger#, P.K. Lai#, M.A. Blanco and C.J. Roberts, Coarse-grained modeling of protein second osmotic virial coefficients: sterics and short-ranged attractions, J. Phys. Chem. B, 117(3):763-770, 2013.

P.K. Lai, C.M. Hsieh and S.T. Lin, Rapid Determination of Entropy and Free Energy of Mixtures from Molecular Dynamics Simulations with the Two-Phase Thermodynamic Model, Phys. Chem. Chem. Phys., 14(43):15206-15213, 2012.

S.T. Lin, L.H. Wang, W.L. Chen, P.K. Lai and C.M. Hsieh, Prediction of miscibility gaps in water/ether mixtures using COSMO-SAC model, Fluid Ph. Equilibria, 310(1-2):19-24,2011.