computer modeling in molecular biology.pdf
computer modeling in molecular biology.pdf
computer modeling in molecular biology.pdf
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Index 243- dynamics 39- hormones 39pp- mediated fold<strong>in</strong>g 176Pharmaceutical applications 44Potential energy 2, 66, 107PRO-CHECK 191PROSITE 15Prote<strong>in</strong>- motion 71- structure prediction lOppProte<strong>in</strong> common core 19, 20Prote<strong>in</strong> evolution 17Prote<strong>in</strong> flexibility and secondarystructure 72Prote<strong>in</strong> fold<strong>in</strong>g 19Prote<strong>in</strong>-loop region 23Prote<strong>in</strong> sequence 10Prote<strong>in</strong>-solvent <strong>in</strong>teraction- with backbone 76, 77- with side-cha<strong>in</strong> 78, 79Prote<strong>in</strong> stability 91RRNA simulationsRadial distribution functions 81Reaction coord<strong>in</strong>ate 217Residue exchange matrices 16Root mean square deviation 18, 71SSCR 22Secondary structure prediction 29Self-diffusion coefficient 82Self-penalty walk (SPW) 219Sequence alignment 11- modification 62Sequence/structure relationship 11,12, 14SHAKE 64Side-cha<strong>in</strong> build<strong>in</strong>g 28Simulation protocol 113Solvent- around RNA 125- dynamical shell 83- explicit treatment 110- implicit treatment 108Sp<strong>in</strong>e of hydration 122Stability mutants 61Stochastic boundary <strong>molecular</strong>dynamics 89Structural environment 16Structural similarity 12, 18Sugar pucker 226SVR 22SWISS PROT 15SYBYL 189, 193Synthetic ion channels 53TTemplate 15Thermodynamic cycle 93, 96Thermodynamics 5Thread<strong>in</strong>g 17TIC 225TIP3P water model 60, 67Transition state 217Transmembrane ion channels 53tRNA 127VValence force field 43Vasopress<strong>in</strong> 44Verlet algorithm 64WWater and nucleic acids 106, 107Water molecules 80- bridges 106, 107, 125-126- structure 80, 82, 106Watson-Crick base-pairs 118XX-ray diffraction 104, 105Xylose isomerase 230
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