PUBLICATIONS

M. Cabreza, W. Hojegian, I.E. Wu and P.K. Lai*, "Predicting Subcutaneous Antibody Bioavailability Using Ensemble Protein Language Models", Mol. Pharm, 22(9):5504–5511, 2025.

L.Y. Huang, P.K. Lai and S.T. Lin, " Physics-guided estimation of mean first-passage times from censored nucleation trajectories", J. Chem. Phys, 163, 044101, 2025.

L. Kalejaye, J.M. Chu, I.E. Wu, B. Amofah, A. Lee, M. Hutchinson, C. Chakiath, A. Dippel, G. Kaplan, M. Damschroder, V. Stanev, M. Pouryahya, M. Boroumand, J. Caldwell, A. Hinton, M. Kreitz, M. Shah, A. Gallegos, N. Mody, and P.K. Lai*, “Accelerating high-concentration monoclonal antibody development with large-scale viscosity data and ensemble deep learning”, mAbs, 17(1):e2483944, 2025.

L.Y. Huang, P.K. Lai and S.T. Lin, "Kinetic analysis of low-barrier nucleation via first-passage time distributions: A CO2 hydrate case study", J. Mol. Liq, 418:126702, 2025.

I.E. Wu, L. Kalejaye and P.K. Lai*, "Machine Learning Models for Predicting Monoclonal Antibody Biophysical Properties from Molecular Dynamics Simulations and Deep Learning-based Surface Descriptors", Mol. Pharm, 22(1):142-153, 2025.

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(10):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.