10 Recent advancement in binding free-energy calculation
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Abhimannu Shome
Abstract
Binding free energy calculation is a crucial method utilized in studying the interactions between ligands and proteins, providing valuable insights into thermodynamics and facilitating rational drug design. Recent progress in computational techniques, force fields, and enhanced sampling approaches has significantly enhanced the accuracy and dependability of these calculations. Furthermore, the integration of machine learning and data-driven methods has further improved predictive capabilities. Quantum mechanical approaches have also been integrated to more precisely account for electronic and quantum effects. These advancements have revolutionized the field, leading to a deeper comprehension of molecular recognition and the development of more efficacious drugs. Ongoing advancements in this area hold immense potential for accelerating the drug discovery process and advancing our understanding of ligand-protein interactions. This chapter explores various types of binding free energy calculation methods including molecular dynamic simulation, Monte Carlo simulation, molecular mechanics/ generalized Born surface area, and molecular mechanics/Poisson-Boltzmann surface area.
Abstract
Binding free energy calculation is a crucial method utilized in studying the interactions between ligands and proteins, providing valuable insights into thermodynamics and facilitating rational drug design. Recent progress in computational techniques, force fields, and enhanced sampling approaches has significantly enhanced the accuracy and dependability of these calculations. Furthermore, the integration of machine learning and data-driven methods has further improved predictive capabilities. Quantum mechanical approaches have also been integrated to more precisely account for electronic and quantum effects. These advancements have revolutionized the field, leading to a deeper comprehension of molecular recognition and the development of more efficacious drugs. Ongoing advancements in this area hold immense potential for accelerating the drug discovery process and advancing our understanding of ligand-protein interactions. This chapter explores various types of binding free energy calculation methods including molecular dynamic simulation, Monte Carlo simulation, molecular mechanics/ generalized Born surface area, and molecular mechanics/Poisson-Boltzmann surface area.
Kapitel in diesem Buch
- Frontmatter I
- Contents V
- 1 Historical development of computer-aided drug design 1
- 2 Lead-hit-based methods for drug design and ligand identification 23
- 3 Virtual screening tools in ligand and receptor-based drug design 51
- 4 State-of-the-art modeling techniques in performing docking algorithms and scoring 65
- 5 Design of computational chiral compounds for drug discovery and development 81
- 6 Role of integrated bioinformatics in structure-based drug design 91
- 7 Molecular recognizable tools in X-ray crystallography in computer-aided drug design 133
- 8 Design of target hit molecules using molecular dynamic simulations: special key aspects of GROMACS or Role of molecular dynamic simulations in designing a hit molecule for drug discovery 151
- 9 Computational prediction of drug-limited solubility and CYP450-mediated biotransformation 175
- 10 Recent advancement in binding free-energy calculation 211
- 11 Role of structural genomics in drug discovery 243
- 12 Unlocking therapeutic potential: computational approaches for enzyme inhibition discovery 295
- 13 Role of spectroscopy in drug discovery 319
- 14 Computer-aided design of peptidomimetic therapeutics 351
- 15 Developing safer therapeutic agents through toxicity prediction 379
- 16 Identifying prominent molecular targets in the fight against drug resistance 403
- Index 429
Kapitel in diesem Buch
- Frontmatter I
- Contents V
- 1 Historical development of computer-aided drug design 1
- 2 Lead-hit-based methods for drug design and ligand identification 23
- 3 Virtual screening tools in ligand and receptor-based drug design 51
- 4 State-of-the-art modeling techniques in performing docking algorithms and scoring 65
- 5 Design of computational chiral compounds for drug discovery and development 81
- 6 Role of integrated bioinformatics in structure-based drug design 91
- 7 Molecular recognizable tools in X-ray crystallography in computer-aided drug design 133
- 8 Design of target hit molecules using molecular dynamic simulations: special key aspects of GROMACS or Role of molecular dynamic simulations in designing a hit molecule for drug discovery 151
- 9 Computational prediction of drug-limited solubility and CYP450-mediated biotransformation 175
- 10 Recent advancement in binding free-energy calculation 211
- 11 Role of structural genomics in drug discovery 243
- 12 Unlocking therapeutic potential: computational approaches for enzyme inhibition discovery 295
- 13 Role of spectroscopy in drug discovery 319
- 14 Computer-aided design of peptidomimetic therapeutics 351
- 15 Developing safer therapeutic agents through toxicity prediction 379
- 16 Identifying prominent molecular targets in the fight against drug resistance 403
- Index 429
