title: Coarse-grained model of proteins incorporating atomistic detail of the active site.
abstract: We present a novel approach to explore the conformational space of globular proteins near their native state. It combines the advantages of coarse-grained models with those of all-atoms simulations, required to treat molecular recognition processes. The comparison between calculated structural properties with those obtained with all-atoms molecular dynamics simulations establishes the accuracy of the model. Our method has the potential to be extended to molecular recognition processes in systems whose characteristic size and time scale prevent an analysis based on all-atoms molecular dynamics.
authors.affiliation: SISSA/ISAS and INFM-DEMOCRITOS Modeling Center, Via Beirut 4, I-34014 Trieste, Italy.
authors.forename: Marilisa
authors.initials: M
authors.lastname: Neri
authors.forename: Claudio
authors.initials: C
authors.lastname: Anselmi
authors.forename: Michele
authors.initials: M
authors.lastname: Cascella
authors.forename: Amos
authors.initials: A
authors.lastname: Maritan
authors.forename: Paolo
authors.initials: P
authors.lastname: Carloni
mesh_terms: D053829:Amyloid Precursor Protein Secretases; D016282:Aspartic Acid Endopeptidases; D001665:Binding Sites; D003198:Computer Simulation; D010450:Endopeptidases / Q000737:chemistry*; D016333:HIV Protease / Q000737:chemistry*; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D055672:Static Electricity; D013269:Stochastic Processes
chemical_list: D053829:Amyloid Precursor Protein Secretases; D010450:Endopeptidases; D016282:Aspartic Acid Endopeptidases; D016333:HIV Protease; C509280:BACE1 protein, human