Over the past  three decades there have been new developments in therapeutic drug design. In Rational Drug Design: Methods and Protocols,  expert researchers in the field detail many of the methodologies used to study rational drug design. These include methods such as virtual screening of chemical hits, rational lead discovery by high throughput screening, combinatorial and fragment based lead generation, peptide based drug discovery, and animal models of lead validation. Written in the highly successful Methods in Molecular Biology¿ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.
 
Authoritative and practical, Rational Drug Design: Methods and Protocols seeks to aid scientists in the further study of rational drug design and future drug discovery.

1. On Setting up and Assessing Docking Simulations for Virtual ScreeningJacek Biesiada, Aleksey Porollo, Jaroslaw Meller 2. Virtual Ligand Screening Combined with NMR to Identify Dvl PDZ Domain Inhibitors Targeting the Wnt SignalingJufang Shan and Jie J. Zheng 3. Rational Design of Rho GTPase Targeting InhibitorsXun Shang and Yi Zheng 4. Rational Design of Peptide Ligands Against a Glycolipid by NMR StudiesWenyong Tong, Tara Sprules, Kalle Gehring, H. Uri Saragovi 5. A Combinatorial Strategy for the Acquisition of Potent and Specific Protein Tyrosine Phosphatase InhibitorsSheng Zhang, Lan Chen, David S. Lawrence and Zhong-Yin Zhang 6. Identification of Allosteric Inhibitors of p21-Activated KinaseJulien Viaud and Jeffrey R. Peterson 7. Using a Modified Yeast Two-hybrid System to Screen for Chemical GEF InhibitorsAnne Blangy and Philippe Fort . 8. Random Mutagenesis of Peptide Aptamers As An Optimization Strategy for Inhibitor ScreeningNathalie Bouquier, Sylvie Fromont, Anne Debant and Susanne Schmidt 9. A Screening Strategy for Trapping the Inactive Conformer of a Dimeric Enzyme with a Small Molecule InhibitorTina Shahian and Charles S. Craik 10. Use of a Fluorescent ATP Analog to Probe the Allosteric Conformational Change in the Active Site of the Protein Kinase PDK1Valerie Hindie, Laura A. Lopez-Garcia, and Ricardo M. Biondi 11. Affinity Purification of Protein Kinases that Adopt a Specific Inactive ConformationPratistha Ranjitkar and Dustin J. Maly 12. Determination of the Kinetics and Thermodynamics of Ligand Binding to a Specific Inactive Conformation in Protein KinasesSanjay B. Hari, Pratistha Ranjitkar and Dustin J. Maly 13. Purification and Specific Assays for Measuring APE-1 Endonuclease ActivityAdrian Esqueda, Mohammed Z Mohammed, Srinivasan Madhusudan, and Nouri Neamati 14. An in vitro Screening to Identify Drug Resistant Mutations for Target-directed Chemotherapeutic AgentsMohammad Azam 15. Utilizing AntagomiR (anti-sense microRNA) to Knock Down microRNA in Murine Bone Marrow CellsChinavenmeni S. Velu and H. Leighton Grimes 16. Synthesis, Conjugation, and Labeling of Multifunctional pRNA Nanoparticles for Specific Delivery of siRNA, Drugs and Other Therapeutics to Target CellsMathieu Cinier, Yi Shu, Daniel Binzel, and Peixuan Guo 17. Mouse Models for Tumor MetastasisShengyu Yang,  J. Jillian Zhang, and Xin-Yun Huang1. On Setting up and Assessing Docking simulations for Virtual ScreeningJacek Biesiada, Aleksey Porollo, Jaroslaw Meller 2. Virtual Ligand Screening Combined with NMR to Identify Dvl PDZ Domain Inhibitors Targeting the Wnt SignalingJufang Shan and Jie J. Zheng 3. Rational Design of Rho GTPase Targeting InhibitorsXun Shang and Yi Zheng 4. Rational Design of Peptide Ligands Against a Glycolipid by NMR StudiesWenyong Tong, Tara Sprules, Kalle Gehring, H. Uri Saragovi 5. A Combinatorial Strategy for the Acquisition of Potent and Specific Protein Tyrosine Phosphatase InhibitorsSheng Zhang, Lan Chen, David S. Lawrence and Zhong-Yin Zhang 6. Identification of Allosteric Inhibitors of p21-Activated KinaseJulien Viaud and Jeffrey R. Peterson 7. Using a Modified Yeast Two-hybrid System to Screen for Chemical GEF InhibitorsAnne Blangy and Philippe Fort . 8. Random Mutagenesis of Peptide Aptamers As An Optimization Strategy for Inhibitor ScreeningNathalie Bouquier, Sylvie Fromont, Anne Debant and Susanne Schmidt 9. A Screening Strategy for Trapping the Inactive Conformer of a Dimeric Enzyme with a Small Molecule InhibitorTina Shahian and Charles S. Craik 10. Use of a Fluorescent ATP Analog to Probe the Allosteric Conformational Change in the Active Site of the Protein Kinase PDK1Valerie Hindie, Laura A. Lopez-Garcia, and Ricardo M. Biondi 11. Affinity Purification of Protein Kinases that Adopt a Specific Inactive ConformationPratistha Ranjitkar and Dustin J. Maly 12. Determination of the Kinetics and Thermodynamics of Ligand Binding to a Specific Inactive Conformation in Protein KinasesSanjay B. Hari, Pratistha Ranjitkar and Dustin J. Maly 13. Purification and Specific Assays for Measuring APE-1 Endonuclease ActivityAdrian Esqueda, Mohammed Z Mohammed, Srinivasan Madhusudan, and Nouri Neamati 14. An in vitro Screening to Identify Drug Resistant Mutations for Target-directed Chemotherapeutic AgentsMohammad Azam 15. Utilizing AntagomiR (anti-sense microRNA) to Knock Down microRNA in Murine Bone Marrow CellsChinavenmeni S. Velu and H. Leighton Grimes 16. Synthesis, Conjugation, and Labeling of Multifunctional pRNA Nanoparticles for Specific Delivery of siRNA, Drugs and Other Therapeutics to Target CellsMathieu Cinier, Yi Shu, Daniel Binzel, and Peixuan Guo 17. Mouse Models for Tumor MetastasisShengyu Yang,  J. Jillian Zhang, and Xin-Yun Huang1. On Setting up and Assessing Docking simulations for Virtual ScreeningJacek Biesiada, Aleksey Porollo, Jaroslaw Meller 2. Virtual Ligand Screening Combined with NMR to Identify Dvl PDZ Domain Inhibitors Targeting the Wnt SignalingJufang Shan and Jie J. Zheng 3. Rational Design of Rho GTPase Targeting InhibitorsXun Shang and Yi Zheng 4. Rational Design of Peptide Ligands Against a Glycolipid by NMR StudiesWenyong Tong, Tara Sprules, Kalle Gehring, H. Uri Saragovi 5. A Combinatorial Strategy for the Acquisition of Potent and Specific Protein Tyrosine Phosphatase InhibitorsSheng Zhang, Lan Chen, David S. Lawrence and Zhong-Yin Zhang 6. Identification of Allosteric Inhibitors of p21-Activated KinaseJulien Viaud and Jeffrey R. Peterson 7. Using a Modified Yeast Two-hybrid System to Screen for Chemical GEF InhibitorsAnne Blangy and Philippe Fort . 8. Random Mutagenesis of Peptide Aptamers As An Optimization Strategy for Inhibitor ScreeningNathalie Bouquier, Sylvie Fromont, Anne Debant and Susanne Schmidt 9. A Screening Strategy for Trapping the Inactive Conformer of a Dimeric Enzyme with a Small Molecule InhibitorTina Shahian and Charles S. Craik 10. Use of a Fluorescent ATP Analog to Probe the Allosteric Conformational Change in the Active Site of the Protein Kinase PDK1Valerie Hindie, Laura A. Lopez-Garcia, and Ricardo M. Biondi 11. Affinity Purification of Protein Kinases that Adopt a Specific Inactive ConformationPratistha Ranjitkar and Dustin J. Maly 12. Determination of the Kinetics and Thermodynamics of Ligand Binding to a Specific Inactive Conformation in Protein KinasesSanjay B. Hari, Pratistha Ranjitkar and Dustin J. Maly 13. Purification and Specific Assays for Measuring APE-1 Endonuclease ActivityAdrian Esqueda, Mohammed Z Mohammed, Srinivasan Madhusudan, and Nouri Neamati 14. An in vitro Screening to Identify Drug Resistant Mutations for Target-directed Chemotherapeutic AgentsMohammad Azam 15. Utilizing AntagomiR (anti-sense microRNA) to Knock Down microRNA in Murine Bone Marrow CellsChinavenmeni S. Velu and H. Leighton Grimes 16. Synthesis, Conjugation, and Labeling of Multifunctional pRNA Nanoparticles for Specific Delivery of siRNA, Drugs and Other Therapeutics to Target CellsMathieu Cinier, Yi Shu, Daniel Binzel, and Peixuan Guo 17. Mouse Models for Tumor MetastasisShengyu Yang,  J. Jillian Zhang, and Xin-Yun Huang