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Intro; Preface; Contents; About the Authors; 1 Brief Introduction; 1.1 Brief Evolutionary History of In Silico Approaches; 1.2 Computational Drug Discovery and Design; 1.3 Epigenetics: Beyond the Sequence; 1.4 Histones Modification; References; 2 Ligand-Based Approach for In-silico Drug Designing; 2.1 Introduction; 2.2 Molecular Descriptors; 2.2.1 2D QSAR Descriptors; 2.2.2 3D QSAR Descriptors; 2.2.3 Multidimensional QSAR; 2.3 Constitutional Descriptors; 2.4 Quantitative Structure-Activity Relationships; 2.5 Molecular Fingerprint and Similarity Searches; 2.6 Similarity Searches in LB-CADD
2.7 Similarity Networks and off Target Predictions2.8 Fingerprint Extensions; 2.9 Computational Methods for Biomolecular Docking; References; 3 Structure-Based Approach for In-silico Drug Designing; 3.1 Introduction; 3.2 Protein Docking; 3.2.1 Protein-Protein Docking; 3.2.2 Protein-Ligand Docking; References; 4 Three-Dimensional (3D) Pharmacophore Modelling-Based Drug Designing by Computational Technique; 4.1 Introduction; 4.1.1 Pharmacophore Model; References; 5 Molecular Dynamics Simulation Approach to Investigate Dynamic Behaviour of System Through the Application of Newtonian Mechanics
5.1 Introduction5.2 Molecular Dynamics Simulations; 5.3 Monte Carlo Research with Metropolis Criterion; References; 6 Receptor Thermodynamics of Ligand-Receptor or Ligand-Enzyme Association; 6.1 Introduction; 6.2 Database Searching; 6.2.1 De Novo Drug Design; 6.3 State-of-the-Art Free Energy Calculations; References; 7 Thermodynamic Cycles and Their Application in Protein Targets; 7.1 Introduction; 7.2 Protein Targets and Applications; 7.3 4-Hydroxyphenylpyruvate Dioxygenase (HPPD); 7.4 Oligopeptide-Binding Protein a (OppA); References; 8 Genomics and Proteomics Using Computational Biology
8.1 Introduction8.2 Peptide Identification; 8.3 De Novo and Hybrid Algorithms; 8.4 Sequence Database Search Algorithms; 8.5 Scoring of Peptide Identifications; 8.6 Peptide-Spectrum Match Scores and Common Thresholds; 8.7 Fundamentals of Gene Transcription and Translation; 8.8 Genome Sequencing; 8.9 Definition of Genome Annotation; 8.10 Genome Annotation Strategies; 8.11 Proteogenomics; References
2.7 Similarity Networks and off Target Predictions2.8 Fingerprint Extensions; 2.9 Computational Methods for Biomolecular Docking; References; 3 Structure-Based Approach for In-silico Drug Designing; 3.1 Introduction; 3.2 Protein Docking; 3.2.1 Protein-Protein Docking; 3.2.2 Protein-Ligand Docking; References; 4 Three-Dimensional (3D) Pharmacophore Modelling-Based Drug Designing by Computational Technique; 4.1 Introduction; 4.1.1 Pharmacophore Model; References; 5 Molecular Dynamics Simulation Approach to Investigate Dynamic Behaviour of System Through the Application of Newtonian Mechanics
5.1 Introduction5.2 Molecular Dynamics Simulations; 5.3 Monte Carlo Research with Metropolis Criterion; References; 6 Receptor Thermodynamics of Ligand-Receptor or Ligand-Enzyme Association; 6.1 Introduction; 6.2 Database Searching; 6.2.1 De Novo Drug Design; 6.3 State-of-the-Art Free Energy Calculations; References; 7 Thermodynamic Cycles and Their Application in Protein Targets; 7.1 Introduction; 7.2 Protein Targets and Applications; 7.3 4-Hydroxyphenylpyruvate Dioxygenase (HPPD); 7.4 Oligopeptide-Binding Protein a (OppA); References; 8 Genomics and Proteomics Using Computational Biology
8.1 Introduction8.2 Peptide Identification; 8.3 De Novo and Hybrid Algorithms; 8.4 Sequence Database Search Algorithms; 8.5 Scoring of Peptide Identifications; 8.6 Peptide-Spectrum Match Scores and Common Thresholds; 8.7 Fundamentals of Gene Transcription and Translation; 8.8 Genome Sequencing; 8.9 Definition of Genome Annotation; 8.10 Genome Annotation Strategies; 8.11 Proteogenomics; References