Bayesian energy landscape tilting: towards concordant models of molecular ensembles.

Supporting Information for Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

FunHunt: model selection based on energy landscape characteristics.

Protein folding and binding is commonly depicted as a search for the minimum energy conformation in a vast energy landscape. Indeed, modelling of protein complex structures by RosettaDock often results in a set of low-energy conformations near the native structure. Ensembles of low-energy conformations can appear, however, in other regions of the energy landscape, especially when backbone movem...

Statistics in the Landscape of Intersecting Brane Models

An approach towards a statistical survey of four dimensional supersymmetric vacua in the string theory landscape is described and illustrated with three examples of ensembles of intersecting D–brane models. The question whether it is conceivable to make predictions based on statistical distributions is discussed. Especially interesting in this context are possible correlations between low energ...

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample heterogeneity. The study of complex macromolecular systems, however, requires an extensive conform...

Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method.

Temperature-based replica-exchange molecular dynamics (REMD), in which multiple simultaneous simulations, or replicas, are run at a range of temperatures, has become increasingly popular for exploring the energy landscape of biomolecular systems. The practical application of REMD toward systems of biomedical interest is often limited by the rapidly increasing number of replicas needed to model ...