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000009867 084__ $$2WoS$$aPhysics, Atomic, Molecular & Chemical
000009867 1001_ $$0P:(DE-Juel1)132024$$aStrodel, B.$$b0$$uFZJ
000009867 245__ $$aInterpolation Schemes for Peptide Rearrangements
000009867 260__ $$aMelville, NY$$bAmerican Institute of Physics$$c2010
000009867 300__ $$a054101
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000009867 440_0 $$03145$$aJournal of Chemical Physics$$v132$$x0021-9606$$y5
000009867 500__ $$aM.B. gratefully acknowledges the Gates Cambridge Trust for financial support.
000009867 520__ $$aA variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures. We also demonstrate the superiority of natural coordinate methods in conjunction with internal alignment. Checking the potential energy of the interpolated structures can act as a criterion for the choice of the interpolation coordinate system, which reduces failures and connection times significantly.
000009867 536__ $$0G:(DE-Juel1)FUEK409$$2G:(DE-HGF)$$aFunktion und Dysfunktion des Nervensystems$$cP33$$x0
000009867 536__ $$0G:(DE-Juel1)FUEK505$$aBioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung$$cP45$$x1
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000009867 650_2 $$2MeSH$$aAlgorithms
000009867 650_2 $$2MeSH$$aArtificial Intelligence
000009867 650_2 $$2MeSH$$aComputer Simulation
000009867 650_2 $$2MeSH$$aImage Enhancement
000009867 650_2 $$2MeSH$$aImage Interpretation, Computer-Assisted
000009867 650_2 $$2MeSH$$aMathematics: methods
000009867 650_2 $$2MeSH$$aMolecular Sequence Data
000009867 650_2 $$2MeSH$$aPattern Recognition, Automated
000009867 650_2 $$2MeSH$$aPeptides: chemistry
000009867 650_2 $$2MeSH$$aProtein Conformation
000009867 650_2 $$2MeSH$$aProtein Folding
000009867 650_2 $$2MeSH$$aThermodynamics
000009867 650_7 $$00$$2NLM Chemicals$$aPeptides
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000009867 7001_ $$0P:(DE-HGF)0$$aBauer, M.S.$$b1
000009867 7001_ $$0P:(DE-HGF)0$$aFejer, S.N.$$b2
000009867 7001_ $$0P:(DE-HGF)0$$aKoslover, E.F.$$b3
000009867 7001_ $$0P:(DE-HGF)0$$aWales, D.J.$$b4
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000009867 8567_ $$uhttp://dx.doi.org/10.1063/1.3273617
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000009867 9131_ $$0G:(DE-Juel1)FUEK505$$bSchlüsseltechnologien$$kP45$$lBiologische Informationsverarbeitung$$vBioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung$$x1
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