Protein interactions: computational methods, analysis and applications
Gespeichert in:
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| Format: | Buch |
| Sprache: | English |
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New Jersey
World Scientific
[2020]
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| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xx, 403 Seiten |
| ISBN: | 9789811211867 |
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Datensatz im Suchindex
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| adam_text | Contents Preface Acknowledgments About the Editor xv xviii xix Part I Protein-Protein Interactions Chapter 1 Structural and dynamical aspects of evolutionarily conserved protein-protein complexes 1 3 Himani Tandon, Sneha Vishwanath and Narayanaswamy Srinivasan 1.1. Introduction 1.2. Evolutionary perspective on protein-protein complexes (PPCs) 1.3. Conservation of structural features of interface residues of interologs 1.4. Protein-protein complexes (PPCs) are fuzzy entities 1.5. Conclusion Acknowledgments References ѴІІ 4 8 14 18 23 24 25
viii Contents Chapter 2 A comprehensive overview of sequence-based protein-binding residue predictions for structured and disordered regions 33 Amita Barik and Lukasz Kurgan 2.1. Introduction 2.2. Computational prediction of protein-binding residues from sequence 2.3. Summary and recommendations Acknowledgments References Chapter 3 Prediction of protein-protein complex structures by docking 34 37 47 48 49 59 Daniai Pourjafar-Dehkordi and Martin Zacharias 3.1. Introduction 3.2. Rigid body protein-protein docking approaches 3.3. Inclusion of protein flexibility during systematic docking searches 3.4. Inclusion of experimental and bioinformatics data during protein-protein docking 3.5. Flexible refinement and final scoring of docked complexes 3.6. Conclusion and fixture developments References Chapter 4 Binding affinity of protein-protein complexes: Experimental techniques, databases and computational methods 59 63 68 70 72 77 78 87 Sherlyn Jemimah, Dugandhar Kumar and M. Michael Gromiha 4.1. Introduction 4.2. Protein-protein binding affinity 4.3. Experimental methods to estimate protein-protein binding affinity 88 89 90
Contents ix 4.4. Important features influencing the bindingaffinity 4.5. Computational resources for binding affinity 4.6. Analysis of PPI networks based on bindingaffinity 4.7. Effect of mutations on binding affinity 4.8. Conclusion Acknowledgments References Chapter 5 Mutational effects on protein-protein interactions 92 95 97 97 103 103 104 109 Jackson Weako, Attila Gursoy and Ozlem Keskin 5.1. 5.2. 5.3. 5.4. 5.5. Introduction Protein-protein interaction and mutation Mutation on PPIs and genetic diseases Mutation in protein interfaces and cancer Experimental measurement of mutational effects on PPIs strength 5.6. Experimental databases 5.7. Computational methods 5.8. Conclusion References Chapter 6 Predicting the consequences of mutations 110 111 117 120 124 125 128 135 135 145 Hemant Kumar and Julia M. Shifman 6.1. Introduction 6.2. Not all mutations are made equal 6.3. Predicting changes in binding free energy due to mutation 6.4. Predicting the effects of post֊translational modifications 6.5. Predictions of coevolving mutations in PPIs 6.6. Applications of computational studies 6.7. Future directions References 146 146 147 152 152 153 155 155
x Contents Part II Protein-Nucleic Acid Interactions Chapter 7 Computational approaches for understanding the recognition mechanism of protein-nucleic acid complexes 167 169 Ambuj Srivastava, Dhanusha Yesudhas, A. Kulandaisamy, Nisba Muralidharan, C. Ramakrishnan, R. Najyarajan and M. Michael Gromiha 7.1. Introduction 7.2. Databases for protein-nucleic acid complexes/ interactions 7.3. Structural analysis of protein-nucleic acid complexes 7.4. Disorder-to-order transition 7.5. Mechanisms for protein-DNA recognition 7.6. Organism-specific recognition of protein-nucleic acid complexes 7.7. Molecular dynamics simulations of protein-nucleic acid complexes 7.8. Binding affinity 7.9. Conclusion Acknowledgments References Chapter 8 Prediction of nudeic acid binding proteins and their binding sites 170 171 177 185 190 197 198 203 205 206 206 217 Dhanusha Yesudhas, Ambuj Srivastava, Nisba Muralidharan, A. Kulandaisamy, R. Nagarajan and M. Michael Gromiha 8.1. Introduction 8.2. Identification of nucleic acid binding proteins 8.3. Specific methods for identifying DNA-binding proteins 8.4. Methods for identifying RNA-binding proteins 8.5. Identification of binding site residues from protein-nucleic acid complex structures 218 220 221 223 227
Contents xi 8.6. Prediction of binding site residues in DNA-binding proteins 8.7. Prediction of binding site residues in RNA-binding proteins 8.8. Best predictor for identifying the binding sites in protein-nucleic acidcomplexes 8.9. Binding site prediction in disordered regions 8.10. Conclusion Acknowledgments References Chapter 9 Predicting protein-binding sites in nucleic acids 228 231 232 233 234 234 234 243 Kyungsook Htm 9.1. Introduction 9.2. Definition of a binding site between proteins and nucleic acids 9.3. Data of binding sites between proteins and nucleic acids 9.4. Predicting protein-binding sites in DNA 9.5. Predicting protein-binding sites in RNA 9.6. Conclusion and future perspective Acknowledgments References Chapter 10 Docking algorithmsand scoring functions 244 246 247 249 250 251 252 252 257 Arina Afanasyeva, Chioko Nagao and Kenji Mizuguchi 10.1. Introduction 10.2. Specificity of protein-RNA/DNA interaction 10.3. Docking algorithms and approaches 10.4. Protein and DNA/RNA flexibility problem 10.5. Conclusion References 257 258 260 266 267 268
xii Contents Chapter 11 Recent progress of methodology development for protein-RNA docking 271 Yun Guo, Xiaoyong Pan and Hong-Bin Shen 11.1. Introduction 11.2. Algorithms of protein-RNA docking 11.3. On existing protein-RNA docking software 11.4. Conclusion and outlook Acknowledgments References Part III Protein-Ligand Interactions Chapter 12 Protein-carbohydrate complexes: Binding site analysis, prediction, binding affinity and molecular dynamics simulations 272 276 286 288 289 289 297 299 K. Veluraja, N. R. Siva Shanmugam J. Jino Blessy, R. A. Jeyamm, B. Lalithamaheswari and M. Michael Gromiha 12.1. Introduction 12.2. Databases for carbohydrates and protein-carbohydrate complexes 12.3. Identification of binding site residues in protein-carbohydrate complexes 12.4. Analysis of binding sites 12.5. Binding affinity 12.6. Prediction of binding site residues 12.7. Molecular dynamics simulations and recognition mechanism 12.8. Applications 12.9. Conclusion Acknowledgments References 300 301 307 308 310 310 Յլշ 322 322 323 շշշ
Contents xiii Chapter 13 Quantitative structure-activity relationship in ligand-based drug design: Concepts and applications 333 Vishnupriya Kanakaveti, P. Anoosba, R. Saktbivel, S.K. Rayala and M. Michael Gromiha 13.1. Introduction 13.2. Goals of QSAR 13.3. Methods based on QSAR 13.4. QSAR based on dimensionality of properties 13.5. QSAR based on correlation and classification 13.6. QSAR model development 13.7. Pitfalls of QSAR modeling 13.8. Pathway for a successful QSAR model 13.9. Applications of QSAR modeling 13.10. Conclusion Acknowledgments References Chapter 14 Protein-ligand interactions in molecular modeling and structure-based drug design 334 335 335 336 337 338 341 341 342 345 345 346 351 Devadasan Velmurugan, Dasararaju Gayathri, Chandrasekaran Ramakrishnan and Atanu Bhattacharjee 14.1. Introduction 14.2. Drug discovery in the past and present 14.3. Flexibility of macromolecular targets 14.4. Sampling of ligands 14.5. Visualization of protein-ligand interactions 14.6. Conclusion and outlook Acknowledgments References 352 353 355 356 362 364 365 365
xiv Contents Chapter 15 An overview of protein-ligand docking and scoring algorithms 371 Ruchika Bbat, Abhilash Jayaraj, Anjali Soni ւmd В. Jayaram 15.1. 15.2. 15.3. 15.4. 15.5. Introduction Docking algorithms Scoring functions for binding free energy estimations CASF, D3R, CASR and other challenges Advantages and pitfalls of machine learning methods 15.6. Summary and perspectives Acknowledgments References Index 372 376 379 382 385 386 389 389 399
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| adam_txt |
Contents Preface Acknowledgments About the Editor xv xviii xix Part I Protein-Protein Interactions Chapter 1 Structural and dynamical aspects of evolutionarily conserved protein-protein complexes 1 3 Himani Tandon, Sneha Vishwanath and Narayanaswamy Srinivasan 1.1. Introduction 1.2. Evolutionary perspective on protein-protein complexes (PPCs) 1.3. Conservation of structural features of interface residues of interologs 1.4. Protein-protein complexes (PPCs) are fuzzy entities 1.5. Conclusion Acknowledgments References ѴІІ 4 8 14 18 23 24 25
viii Contents Chapter 2 A comprehensive overview of sequence-based protein-binding residue predictions for structured and disordered regions 33 Amita Barik and Lukasz Kurgan 2.1. Introduction 2.2. Computational prediction of protein-binding residues from sequence 2.3. Summary and recommendations Acknowledgments References Chapter 3 Prediction of protein-protein complex structures by docking 34 37 47 48 49 59 Daniai Pourjafar-Dehkordi and Martin Zacharias 3.1. Introduction 3.2. Rigid body protein-protein docking approaches 3.3. Inclusion of protein flexibility during systematic docking searches 3.4. Inclusion of experimental and bioinformatics data during protein-protein docking 3.5. Flexible refinement and final scoring of docked complexes 3.6. Conclusion and fixture developments References Chapter 4 Binding affinity of protein-protein complexes: Experimental techniques, databases and computational methods 59 63 68 70 72 77 78 87 Sherlyn Jemimah, Dugandhar Kumar and M. Michael Gromiha 4.1. Introduction 4.2. Protein-protein binding affinity 4.3. Experimental methods to estimate protein-protein binding affinity 88 89 90
Contents ix 4.4. Important features influencing the bindingaffinity 4.5. Computational resources for binding affinity 4.6. Analysis of PPI networks based on bindingaffinity 4.7. Effect of mutations on binding affinity 4.8. Conclusion Acknowledgments References Chapter 5 Mutational effects on protein-protein interactions 92 95 97 97 103 103 104 109 Jackson Weako, Attila Gursoy and Ozlem Keskin 5.1. 5.2. 5.3. 5.4. 5.5. Introduction Protein-protein interaction and mutation Mutation on PPIs and genetic diseases Mutation in protein interfaces and cancer Experimental measurement of mutational effects on PPIs strength 5.6. Experimental databases 5.7. Computational methods 5.8. Conclusion References Chapter 6 Predicting the consequences of mutations 110 111 117 120 124 125 128 135 135 145 Hemant Kumar and Julia M. Shifman 6.1. Introduction 6.2. Not all mutations are made equal 6.3. Predicting changes in binding free energy due to mutation 6.4. Predicting the effects of post֊translational modifications 6.5. Predictions of coevolving mutations in PPIs 6.6. Applications of computational studies 6.7. Future directions References 146 146 147 152 152 153 155 155
x Contents Part II Protein-Nucleic Acid Interactions Chapter 7 Computational approaches for understanding the recognition mechanism of protein-nucleic acid complexes 167 169 Ambuj Srivastava, Dhanusha Yesudhas, A. Kulandaisamy, Nisba Muralidharan, C. Ramakrishnan, R. Najyarajan and M. Michael Gromiha 7.1. Introduction 7.2. Databases for protein-nucleic acid complexes/ interactions 7.3. Structural analysis of protein-nucleic acid complexes 7.4. Disorder-to-order transition 7.5. Mechanisms for protein-DNA recognition 7.6. Organism-specific recognition of protein-nucleic acid complexes 7.7. Molecular dynamics simulations of protein-nucleic acid complexes 7.8. Binding affinity 7.9. Conclusion Acknowledgments References Chapter 8 Prediction of nudeic acid binding proteins and their binding sites 170 171 177 185 190 197 198 203 205 206 206 217 Dhanusha Yesudhas, Ambuj Srivastava, Nisba Muralidharan, A. Kulandaisamy, R. Nagarajan and M. Michael Gromiha 8.1. Introduction 8.2. Identification of nucleic acid binding proteins 8.3. Specific methods for identifying DNA-binding proteins 8.4. Methods for identifying RNA-binding proteins 8.5. Identification of binding site residues from protein-nucleic acid complex structures 218 220 221 223 227
Contents xi 8.6. Prediction of binding site residues in DNA-binding proteins 8.7. Prediction of binding site residues in RNA-binding proteins 8.8. Best predictor for identifying the binding sites in protein-nucleic acidcomplexes 8.9. Binding site prediction in disordered regions 8.10. Conclusion Acknowledgments References Chapter 9 Predicting protein-binding sites in nucleic acids 228 231 232 233 234 234 234 243 Kyungsook Htm 9.1. Introduction 9.2. Definition of a binding site between proteins and nucleic acids 9.3. Data of binding sites between proteins and nucleic acids 9.4. Predicting protein-binding sites in DNA 9.5. Predicting protein-binding sites in RNA 9.6. Conclusion and future perspective Acknowledgments References Chapter 10 Docking algorithmsand scoring functions 244 246 247 249 250 251 252 252 257 Arina Afanasyeva, Chioko Nagao and Kenji Mizuguchi 10.1. Introduction 10.2. Specificity of protein-RNA/DNA interaction 10.3. Docking algorithms and approaches 10.4. Protein and DNA/RNA flexibility problem 10.5. Conclusion References 257 258 260 266 267 268
xii Contents Chapter 11 Recent progress of methodology development for protein-RNA docking 271 Yun Guo, Xiaoyong Pan and Hong-Bin Shen 11.1. Introduction 11.2. Algorithms of protein-RNA docking 11.3. On existing protein-RNA docking software 11.4. Conclusion and outlook Acknowledgments References Part III Protein-Ligand Interactions Chapter 12 Protein-carbohydrate complexes: Binding site analysis, prediction, binding affinity and molecular dynamics simulations 272 276 286 288 289 289 297 299 K. Veluraja, N. R. Siva Shanmugam J. Jino Blessy, R. A. Jeyamm, B. Lalithamaheswari and M. Michael Gromiha 12.1. Introduction 12.2. Databases for carbohydrates and protein-carbohydrate complexes 12.3. Identification of binding site residues in protein-carbohydrate complexes 12.4. Analysis of binding sites 12.5. Binding affinity 12.6. Prediction of binding site residues 12.7. Molecular dynamics simulations and recognition mechanism 12.8. Applications 12.9. Conclusion Acknowledgments References 300 301 307 308 310 310 Յլշ 322 322 323 շշշ
Contents xiii Chapter 13 Quantitative structure-activity relationship in ligand-based drug design: Concepts and applications 333 Vishnupriya Kanakaveti, P. Anoosba, R. Saktbivel, S.K. Rayala and M. Michael Gromiha 13.1. Introduction 13.2. Goals of QSAR 13.3. Methods based on QSAR 13.4. QSAR based on dimensionality of properties 13.5. QSAR based on correlation and classification 13.6. QSAR model development 13.7. Pitfalls of QSAR modeling 13.8. Pathway for a successful QSAR model 13.9. Applications of QSAR modeling 13.10. Conclusion Acknowledgments References Chapter 14 Protein-ligand interactions in molecular modeling and structure-based drug design 334 335 335 336 337 338 341 341 342 345 345 346 351 Devadasan Velmurugan, Dasararaju Gayathri, Chandrasekaran Ramakrishnan and Atanu Bhattacharjee 14.1. Introduction 14.2. Drug discovery in the past and present 14.3. Flexibility of macromolecular targets 14.4. Sampling of ligands 14.5. Visualization of protein-ligand interactions 14.6. Conclusion and outlook Acknowledgments References 352 353 355 356 362 364 365 365
xiv Contents Chapter 15 An overview of protein-ligand docking and scoring algorithms 371 Ruchika Bbat, Abhilash Jayaraj, Anjali Soni ւmd В. Jayaram 15.1. 15.2. 15.3. 15.4. 15.5. Introduction Docking algorithms Scoring functions for binding free energy estimations CASF, D3R, CASR and other challenges Advantages and pitfalls of machine learning methods 15.6. Summary and perspectives Acknowledgments References Index 372 376 379 382 385 386 389 389 399 |
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| publisher | World Scientific |
| record_format | marc |
| spelling | Protein interactions computational methods, analysis and applications editor M. Michael Gromiha, Indian Institute of Technology Madras, India New Jersey World Scientific [2020] © 2020 xx, 403 Seiten txt rdacontent n rdamedia nc rdacarrier Protein-Protein-Wechselwirkung (DE-588)4745193-2 gnd rswk-swf RNS (DE-588)4076759-0 gnd rswk-swf Wechselwirkung (DE-588)4064937-4 gnd rswk-swf Kohlenhydrate (DE-588)4164517-0 gnd rswk-swf Ligand (DE-588)4035711-9 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf Protein-Protein-Wechselwirkung (DE-588)4745193-2 s DE-604 Proteine (DE-588)4076388-2 s DNS (DE-588)4070512-2 s RNS (DE-588)4076759-0 s Kohlenhydrate (DE-588)4164517-0 s Ligand (DE-588)4035711-9 s Wechselwirkung (DE-588)4064937-4 s Gromiha, M. Michael 1967- (DE-588)174035357 edt Erscheint auch als Online-Ausgabe 978-981-121-187-4 Erscheint auch als Online-Ausgabe 978-981-121-188-1 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=032266196&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Protein interactions computational methods, analysis and applications Protein-Protein-Wechselwirkung (DE-588)4745193-2 gnd RNS (DE-588)4076759-0 gnd Wechselwirkung (DE-588)4064937-4 gnd Kohlenhydrate (DE-588)4164517-0 gnd Ligand (DE-588)4035711-9 gnd DNS (DE-588)4070512-2 gnd Proteine (DE-588)4076388-2 gnd |
| subject_GND | (DE-588)4745193-2 (DE-588)4076759-0 (DE-588)4064937-4 (DE-588)4164517-0 (DE-588)4035711-9 (DE-588)4070512-2 (DE-588)4076388-2 |
| title | Protein interactions computational methods, analysis and applications |
| title_auth | Protein interactions computational methods, analysis and applications |
| title_exact_search | Protein interactions computational methods, analysis and applications |
| title_exact_search_txtP | Protein interactions computational methods, analysis and applications |
| title_full | Protein interactions computational methods, analysis and applications editor M. Michael Gromiha, Indian Institute of Technology Madras, India |
| title_fullStr | Protein interactions computational methods, analysis and applications editor M. Michael Gromiha, Indian Institute of Technology Madras, India |
| title_full_unstemmed | Protein interactions computational methods, analysis and applications editor M. Michael Gromiha, Indian Institute of Technology Madras, India |
| title_short | Protein interactions |
| title_sort | protein interactions computational methods analysis and applications |
| title_sub | computational methods, analysis and applications |
| topic | Protein-Protein-Wechselwirkung (DE-588)4745193-2 gnd RNS (DE-588)4076759-0 gnd Wechselwirkung (DE-588)4064937-4 gnd Kohlenhydrate (DE-588)4164517-0 gnd Ligand (DE-588)4035711-9 gnd DNS (DE-588)4070512-2 gnd Proteine (DE-588)4076388-2 gnd |
| topic_facet | Protein-Protein-Wechselwirkung RNS Wechselwirkung Kohlenhydrate Ligand DNS Proteine |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=032266196&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT gromihammichael proteininteractionscomputationalmethodsanalysisandapplications |