Rational Drug Design, Softcover reprint of the original 1st ed. 2012 Methods and Protocols Methods in Molecular Biology Series, Vol. 928

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 Screening

Jacek Biesiada, Aleksey Porollo, Jaroslaw Meller

2. Virtual Ligand Screening Combined with NMR to Identify Dvl PDZ Domain Inhibitors Targeting the Wnt Signaling

Jufang Shan and Jie J. Zheng

3. Rational Design of Rho GTPase Targeting Inhibitors

Xun Shang and Yi Zheng

Wenyong Tong, Tara Sprules, Kalle Gehring, H. Uri Saragovi

5. A Combinatorial Strategy for the Acquisition of Potent and Specific Protein Tyrosine Phosphatase Inhibitors

Sheng Zhang, Lan Chen, David S. Lawrence and Zhong-Yin Zhang

6. Identification of Allosteric Inhibitors of p21-Activated Kinase

Julien Viaud and Jeffrey R. Peterson

8. Random Mutagenesis of Peptide Aptamers As An Optimization Strategy for Inhibitor Screening

Nathalie 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 Inhibitor

Tina 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 PDK1

Valerie Hindie, Laura A. Lopez-Garcia, and Ricardo M. Biondi

13. Purification and Specific Assays for Measuring APE-1 Endonuclease Activity

Adrian Esqueda, Mohammed Z Mohammed, Srinivasan Madhusudan, and Nouri Neamati

14. An in vitro Screening to Identify Drug Resistant Mutations for Target-directed Chemotherapeutic Agents

Mohammad Azam

15. Utilizing AntagomiR (anti-sense microRNA) to Knock Down microRNA in Murine Bone Marrow Cells

Chinavenmeni 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 Cells

Mathieu Cinier, Yi Shu, Daniel Binzel, and Peixuan Guo

17. Mouse Models for Tumor Metastasis

Shengyu Yang,  J. Jillian Zhang, and Xin-Yun Huang

1. On Setting up and Assessing Docking simulations for Virtual Screening

Jacek Biesiada, Aleksey Porollo, Jaroslaw Meller

2. Virtual Ligand Screening Combined with NMR to Identify Dvl PDZ Domain Inhibitors Targeting the Wnt Signaling

Jufang Shan and Jie J. Zheng

3. Rational Design of Rho GTPase Targeting Inhibitors

Xun Shang and Yi Zheng

Wenyong Tong, Tara Sprules, Kalle Gehring, H. Uri Saragovi

5. A Combinatorial Strategy for the Acquisition of Potent and Specific Protein Tyrosine Phosphatase Inhibitors

Sheng Zhang, Lan Chen, David S. Lawrence and Zhong-Yin Zhang

6. Identification of Allosteric Inhibitors of p21-Activated Kinase

Julien Viaud and Jeffrey R. Peterson

8. Random Mutagenesis of Peptide Aptamers As An Optimization Strategy for Inhibitor Screening

Nathalie 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 Inhibitor

Tina 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 PDK1

Valerie Hindie, Laura A. Lopez-Garcia, and Ricardo M. Biondi

13. Purification and Specific Assays for Measuring APE-1 Endonuclease Activity

Adrian Esqueda, Mohammed Z Mohammed, Srinivasan Madhusudan, and Nouri Neamati

14. An in vitro Screening to Identify Drug Resistant Mutations for Target-directed Chemotherapeutic Agents

Mohammad Azam

15. Utilizing AntagomiR (anti-sense microRNA) to Knock Down microRNA in Murine Bone Marrow Cells

Chinavenmeni 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 Cells

Mathieu Cinier, Yi Shu, Daniel Binzel, and Peixuan Guo

17. Mouse Models for Tumor Metastasis

Shengyu Yang,  J. Jillian Zhang, and Xin-Yun Huang

1. On Setting up and Assessing Docking simulations for Virtual Screening

Jacek Biesiada, Aleksey Porollo, Jaroslaw Meller

2. Virtual Ligand Screening Combined with NMR to Identify Dvl PDZ Domain Inhibitors Targeting the Wnt Signaling

Jufang Shan and Jie J. Zheng

3. Rational Design of Rho GTPase Targeting Inhibitors

Xun Shang and Yi Zheng

Wenyong Tong, Tara Sprules, Kalle Gehring, H. Uri Saragovi

5. A Combinatorial Strategy for the Acquisition of Potent and Specific Protein Tyrosine Phosphatase Inhibitors

Sheng Zhang, Lan Chen, David S. Lawrence and Zhong-Yin Zhang

6. Identification of Allosteric Inhibitors of p21-Activated Kinase

Julien Viaud and Jeffrey R. Peterson

8. Random Mutagenesis of Peptide Aptamers As An Optimization Strategy for Inhibitor Screening

Nathalie 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 Inhibitor

Tina 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 PDK1

Valerie Hindie, Laura A. Lopez-Garcia, and Ricardo M. Biondi

13. Purification and Specific Assays for Measuring APE-1 Endonuclease Activity

Adrian Esqueda, Mohammed Z Mohammed, Srinivasan Madhusudan, and Nouri Neamati

14. An in vitro Screening to Identify Drug Resistant Mutations for Target-directed Chemotherapeutic Agents

Mohammad Azam

15. Utilizing AntagomiR (anti-sense microRNA) to Knock Down microRNA in Murine Bone Marrow Cells

Chinavenmeni 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 Cells

Mathieu Cinier, Yi Shu, Daniel Binzel, and Peixuan Guo

17. Mouse Models for Tumor Metastasis

Shengyu Yang,  J. Jillian Zhang, and Xin-Yun Huang

Aids scienctist in further study of rational drug design

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Includes supplementary material: sn.pub/extras

Includes supplementary material: sn.pub/extras