Computational Methods for Estimating the Kinetic Parameters of Biological Systems

1. Current Approaches of Building Mechanistic Pharmacodynamic Drug-Target Binding Models

Jingyi Liang, Vi Ngoc-Nha Tran, Colin Hemez, and Pia Abel zur Wiesch



2. An Extended Model Including Target Turnover, Ligand-Target Complex Kinetics, and Binding Properties to Describe Drug-Receptor Interactions

Lambertus A. Peletier



3. Beyond the Michaelis-Menten: Bayesian Inference for Enzyme Kinetic Analysis

Hyukpyo Hong, Boseung Choi, and Jae Kyoung Kim



4. Multi-Objective Optimization Tuning Framework for Kinetic Parameter Selection and Estimation

Yadira Boada, Jes?s Pic?, and Alejandro Vignoni



5. Relationship between Dimensionality and Convergence of Optimization Algorithms: A Comparison between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI

Andrea Degasperi, Lan K. Nguyen, Dirk Fey, and Boris N. Kholodenko



6. Dynamic Optimization Approach to Estimate Kinetic Parameters of Monod-Based Microalgae Growth Models

Siti S. Jamaian, Fathul H. Zulkifli, and Kim S. Ling



7. Automatic Assembly and Calibration of Models of Enzymatic Reactions Based on Ordinary Differential Equations

Jure Stojan, Milan Hodoscek, and Dusanka Janezic



8. Data Processing to Probe the Cellular Hydrogen Peroxide Landscape

Fernando Antunes and Paula Brito



9. Computational Methods for Structure-Based Drug Design through Systems Biology

Aman Chandra Kaushik, Shakti Sahi, and Dong-Qing Wei



10. Model Setup and Procedures for Prediction of Enzyme Reaction Kinetics with QM-Only and QM: MM Approaches

Michal Glanowski, Sangita Kachhap, Tomasz Borowski, and Maciej Szaleniec



11. The Role of Ligand Rebinding and Facilitated Dissociation on the Characterization of Dissociation Rates by Surface Plasmon Resonance (SPR) and Benchmarking Performance Metrics

Aykut Erbas and Fatih Inci



12. Computational Tools for Accurate Binding Free Energy Prediction

Maria M. Reif and Martin Zacharias



13. Computational Alanine Scanning Reveals Common Features of TCR/pMHC Recognition in HLA-DQ8-Associated Celiac Disease

Linqiong Qiu, Jianing Song, and John Z.H. Zhang



14. Umbrella Sampling-Based Method to Compute Ligand-Binding Affinity

Son Tung Ngo and Minh Quan Pham



15. Creating Maps of the Ligand Binding Landscape for Kinetics-Based Drug Discovery

Tom Dixon, Samuel D. Lotz, and Alex Dickson



16. Prediction of Protein-Protein Binding Affinities from Unbound Protein Structures

&nb