Computational Methods for Estimating the Kinetic Parameters of Biological Systems
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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 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 Hodosček, and Dusanka Janezič
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 Erbaş 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
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