Computational Methods for Estimating the Kinetic Parameters of Biological Systems

Front Matter

Current Approaches of Building Mechanistic Pharmacodynamic Drug–Target Binding Models

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

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

• Lambertus A. Peletier

Beyond the Michaelis–Menten: Bayesian Inference for Enzyme Kinetic Analysis

• Hyukpyo Hong, Boseung Choi, Jae Kyoung Kim

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

• Yadira Boada, Jesús Picó, Alejandro Vignoni

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, Boris N. Kholodenko

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

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

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

• Jure Stojan, Milan Hodošček, Dušanka Janežič

Data Processing to Probe the Cellular Hydrogen Peroxide Landscape

• Fernando Antunes, Paula Brito

Computational Methods for Structure-Based Drug Design Through System Biology

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

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

• Michał Glanowski, Sangita Kachhap, Tomasz Borowski, Maciej Szaleniec

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, Fatih Inci

Computational Tools for Accurate Binding Free-Energy Prediction

• Maria M. Reif, Martin Zacharias

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

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

Umbrella Sampling-Based Method to Compute Ligand-Binding Affinity

• Son Tung Ngo, Minh Quan Pham

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

• Tom Dixon, Samuel D. Lotz, Alex Dickson

Prediction of Protein–Protein Binding Affinities from Unbound Protein Structures

• Alberto Meseguer, Patricia Bota, Narcis Fernández-Fuentes, Baldo Oliva

Parameter Optimization for Ion Channel Models: Integrating New Data with Known Channel Properties

• Marco A. Navarro, Marzie Amirshenava, Autoosa Salari, Mirela Milescu, Lorin S. Milescu

Back Matter