Molecular Modeling & Simulation - Nano Mahidol - Mahidol University

More documents

Recommendations

Info

2. AlignmentHomology modellingIssara SramalaStep 2: Align SequencesQueryHit #1Hit #2ACDEFGHIKLMNPQRST--FGHQWERT-----TYREWYEGASDEYAHLRILDPQRSTVAYAYE--KSFAPPGSFKWEYEAMCDEYAHIRLMNPERSTVAGGHQWERT----GSFKEWYAA• Key step in Homology Modelling• Small error in alignment can leadto big error in structural model• Multiple alignments are usuallybetter than pairwise alignmentsHit #1 Hit #2Homology modelling2. AlignmentIssara Sramala• Regions in the homologous proteins that arestructurally/functionally important are moreconserved (i.e. have little sequence variation) in the1º AA sequence than the regions, which are not asrelevant for protein folding and function.• Similar region often called SCR (structurallyconserver regions)• Variable regions called VRs or SVR (for variableregions)
Homology modelling2. AlignmentIssara SramalaSCR #1SCR’sSCR #2QueryHit #1Hit #2ACDEFGHIKLMNPQRST--FGHQWERT-----TYREWYEGASDEYAHLRILDPQRSTVAYAYE--KSFAPPGSFKWEYEAMCDEYAHIRLMNPERSTVAGGHQWERT----GSFKEWYAAHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCBBBBBBBBBHit #1 Hit #2• Corresponds to the most stablestructures or regions (usuallyinterior) of protein• Corresponds to sequence regionswith lowest level of gapping,highest level of sequenceconservation• Usually corresponds tosecondary structuresQueryHit #1Hit #2SVR’sACDEFGHIKLMNPQRST--FGHQWERT-----TYREWYEGASDEYAHLRILDPQRSTVAYAYE--KSFAPPGSFKWEYEAMCDEYAHIRLMNPERSTVAGGHQWERT----GSFKEWYAAHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCBBBBBBBBBHit #1 Hit #2SVR (loop)Homology modelling2. AlignmentIssara Sramala• Corresponds to the least stableor most flexible regions (usuallyexterior) of protein• Highest level of gapping, lowestlevel of sequence conservation• Usually corresponds to loopsand turns
Page 4: Atomistic Model• Quantum Mechanic
Page 8 and 9: Molecular MechanicsNanoscience Mahi
Page 10 and 11: Molecular MechanicsMolecular Modeli
Page 12 and 13: Molecular MechanicsNanoscience Mahi
Page 14 and 15: Molecular MechanicsMolecular Modeli
Page 17: Wire FrameMolecular ModelingBPTIPro
Page 20 and 21: Line RibbonMolecular ModelingBPTIPr
Page 22 and 23: Model & MethodMolecular ModelingMOD
Page 24 and 25: HomologyBasic Steps in Homology Mod
Page 28 and 29: Generate Core CoordinatesHomology m
Page 32 and 33: 4. Energy MinimizationBad modelsHom
Page 34: ValidationHomology modellingStructu
Page 37 and 38: Molecular DynamicsMolecular Modelin
Page 39 and 40: Simulation in WaterMolecular Modeli
Page 41: Homology Model of Bt Cry4BMolecular
Page 44 and 45: Bt Cry4B in WaterMolecular Modeling

Molecular Modeling & Simulation - Nano Mahidol - Mahidol University

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?