mAbs, see Monoclonal antibodies MACS, 99
Major histocompatibility complex (MHC) proteins, 167 cell surface display, 167-168 peptide-MHC complexes, 167 phage display, 167 single-chain, 30 Malate dehydrogenase (MDH), 315 Maltose-binding protein (MBP), 118 MBP, see Maltose-binding protein MCB, see Monochlorobimane MC method, see Monte Carlo method MCQ, see Quenched MC MCSA, see Monte Carlo simulated annealing MDH, see Malate dehydrogenase Mean field biased Monte Carlo (MFBMC), 296 Mechanism-based inhibitors, 64 Messenger RNA (mRNA), 52 display, 66-69
advantages and limitations among cellfree methods, 68 history, advances, and applications, 67 technical description, 66 -protein fusion, 67 Metal-assisted protein assembly, 245 Metal-binding site, geometric definition of, 345 Methanococcus jannaschii, 134, 208 Metropolis Monte Carlo, 349 MFBMC, see Mean field biased Monte Carlo MHC class II molecules, 158 MHC proteins, see Major histocompatibility proteins Microbead display, 73 Model(s)
accuracy, rotamer library, 288 backbone flexibility, 329 ball and stick, 283 generalized Born, 270 Poisson-Boltzmann, 288 van der Waals force, 348 vdW repulsions, 314 Modular protein design, 181 Molecular display technologies, 112 Molecular force fields, 257-279 ACCESS program, 267 atomic solvation parameter, 265 cavity formation, 266 charge density, 269 Coulomb's law, 263, 268 Debye-Huckel theory, 269
different definitions of protein surface, 268 equilibrium bond length, 262 foldability of protein sequence, 271 free energy of denatured protein, 260 generalized Born model, 270 Gibbs free energy, 266 inclusion-exclusion formula, 268 log-odd potentials, 271 most common force fields, 264 NACCESS program, 267 nonpolar solvation free energy, 267 partition function problem, 273 perspectives, 275-276 physics-based force fields, 258-270
computing of free energy with explicit water representation, 261-264 computing of free energy with implicit solvent representation, 264-270 denatured state, 260-261 entropy, 264 internal energy, 261-264 nonpolar contribution to Wsoi, 265-268 polar contribution to Wso, 268-270 potential of mean forces, 264-265 stability of protein sequences (application to sequence design), 259-260 Poisson-Boltzmann equation, 266 Poisson's law, 269 potentials of mean force, 272 Protein Data Bank, 257 protein-folding problem, 258 reference state, 273 solvation free energy, 266 statistical potentials, 270-275 other statistical potentials, 275 potential of mean force, 272-273 reference state, 273-275 surface area model, 266, 267 thermodynamics, 260 types of bonded interactions, 261 zero-energy state, 273 Molecular scaffold concept, 110-111 Monochlorobimane (MCB), 134 Monoclonal antibodies (mAbs), 154 against IL-2 receptor, 165 against von Willebrand factor, 302 FDA approval of, 154 GFP variant recognized by, 11 hybridoma methods, 8 neutralizing, 35 nicotine-specific scFvs, 36 therapeutics, 161 Monte Carlo (MC) method, 295 Monte Carlo simulated annealing (MCSA), 296 mRNA, see Messenger RNA MSA, see Multiple sequence alignments Multiple sequence alignments (MSA), 383
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Do we really want the one thing that gives us its resources unconditionally to suffer even more than it is suffering now? Nature, is a part of our being from the earliest human days. We respect Nature and it gives us its bounty, but in the recent past greedy money hungry corporations have made us all so destructive, so wasteful.