0000000000297582

AUTHOR

Donna Bassolino-klimas

showing 3 related works from this author

Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints

1996

A new functional representation of NMR-derived distance constraints, the flexible restraint potential, has been implemented in the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168) for molecular structure generation. In addition, flat-bottomed restraint potentials for representing dihedral angle and vicinal scalar coupling constraints have been introduced into CONGEN. An effective simulated annealing (SA) protocol that combines both weight annealing and temperature annealing is described. Calculations have been performed using ideal simulated NMR constraints, in order to evaluate the use of restrained molecular dynamics (MD) with these target functions as implemented i…

Coupling constantQuantitative Biology::BiomoleculesChemistryCrambinNuclear magnetic resonance spectroscopyDihedral angleEnergy minimizationBiochemistryMolecular physicsMaxima and minimaMolecular dynamicsCrystallographySimulated annealingMolecular BiologyProtein Science
researchProduct

Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predi…

1997

We have developed an automatic approach for homology modeling using restrained molecular dynamics and simulated annealing procedures, together with conformational search algorithms available in the molecular mechanics program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168). The accuracy of the method is validated by "predicting" structures of two homeodomain proteins with known three-dimensional structures, and then applied to predict the three-dimensional structure of the homeodomain of the murine Msx-1 transcription factor. Regions of the unknown protein structure that are highly homologous to the known template structure are constrained by "homology distance constraints,"…

Models MolecularSaccharomyces cerevisiae ProteinsProtein ConformationMSX1 Transcription FactorMolecular Sequence DataSaccharomyces cerevisiaeBiologyProtein EngineeringBiochemistryProtein Structure SecondaryMolecular dynamicsMiceProtein structureAnimalsComputer SimulationHomology modelingAmino Acid SequenceMolecular BiologyHomeodomain ProteinsMSX1 Transcription FactorSequence Homology Amino AcidNuclear ProteinsProtein engineeringProtein superfamilyengrailedRepressor ProteinsCrystallographyAntennapedia Homeodomain ProteinThreading (protein sequence)AlgorithmsInformation SystemsTranscription FactorsResearch ArticleProtein science : a publication of the Protein Society
researchProduct

Simulated annealing with restrained molecular dynamics using CONGEN: Energy refinement of the NMR solution structures of epidermal and type-αtransfor…

1996

The new functionality of the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168; Bassolino-Klimas D et al., 1996, Protein Sci 5:593-603) has been applied for energy refinement of two previously determined solution NMR structures, murine epidermal growth factor (mEGF) and human type-alpha transforming growth factor (hTGF alpha). A summary of considerations used in converting experimental NMR data into distance constraints for CONGEN is presented. A general protocol for simulated annealing with restrained molecular dynamics is applied to generate NMR solution structures using CONGEN together with real experimental NMR data. A total of 730 NMR-derived constraints for mEGF a…

Maxima and minimaMolecular dynamicsCrystallographyProtein structureChemistrySimulated annealingMoleculeNuclear magnetic resonance spectroscopyProtein superfamilyType (model theory)Molecular BiologyBiochemistryProtein Science
researchProduct