annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small b sheet containing proteins. Most of the simulated structures have native-like solvent accessibility and secondary structure patterns, and thus ensembles

is determined from a representative set of experimental protein structures. The amino acid solvent accessible surface area (SASA) is estimated with a neighbor vector measure that increases in accuracy compared to the neighbor count measure while remaining pairwise decomposable [Durham, E., et al. (2009) J. Mol

structure refinement Determining an accurate initial native-like protein fold is one of the most important and time-consuming steps of de novo NMR structure determination. Here we demonstrate that high-quality native-like models can be rapidly generated from initial structures obtained using

and if certain types of cues are more accessible than others. The results reveal qualitative differences in the underlying linguistic knowledge of early vs. late bilinguals with heritage language learners (i.e., early bilinguals) achieving a higher level of mastery than second language learners (i.e., late

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Knowingthecoordinationnumber andrelativesolventaccessibilityofalltheresidues inaproteiniscrucialforderivingconstraintsuseful inmodelingproteinfoldingandproteinstructure andinscoringremotehomologysearches.Wedevelopensemblesofbidirectionalrecurrentneural networkarchitecturestoimprovethestateofthe artinbothcontactandaccessibilityprediction, leveragingalargecorpusofcurateddatatogether withevolutionaryinformation.Theensemblesare usedtodiscriminatebetweentwodifferentstatesof residuecontactsorrelativesolventaccessibility, higherorlowerthanathresholddeterminedbythe averagevalueoftheresiduedistributionorthe accessibilitycutoff.Forcoordinationnumbers,the ensembleachievesperformancesrangingwithin 70.6--73.9%dependingontheradiusadoptedtodiscriminatecontacts (6--12).Theseperformances representgainsof16--20%overthebaselinestatisticalpredictor, alwaysassigninganaminoacidtothe largestclass,andare4--7%betterthananyprevious method.Acombinationofdifferentradiuspredictorsfurtherimprovesperformance. Foraccessibilitythresholdsintherelevant15 --30%range,the ensembleconsistentlyachievesaperformanceabove 77%,whichis10--16%abovethebaselineprediction andbetterthanotherexistingpredictors,byupto severalpercentagepoints.Forbothproblems,we quantifytheimprovementduetoevolutionaryinformationintheformofPSI -BLAST-generatedprofiles overBLASTprofiles.Thepredictionprogramsare implementedintheformoftwowebservers,CONproandACCpro, availableathttp://promoter.ics. uci.edu/BRNN-PRED/.Proteins2002;47:142--153.

Summary: Protein secondary structure and solvent accessibility pre-dictions are a fundamental intermediate step towards protein structure and function prediction. We present new systems for the ab initio prediction of protein secondary structure and solvent accessibility, Porter 4.0 and PaleAle 4

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effects on the structure-property relationship of anticonvulsant hydantoin derivatives: A solvatochromic analysis

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