The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins

@article{citeulike:1093615, author = {Richter and Barbara and Gsponer and Joerg and Varnai and Peter and Salvatella and Xavier and Vendruscolo and Michele}, citeulike-article-id = {1093615}, comment = {How do they enforce the restraints over pairs or over 16 replicas in the energy function? Do they compute the energy at each step or at the end of each cycle? ---=note-separator=--- They actually do simulated annealing on the replicas, and play with the force constants as well as the temperature in this annealing procedure. They vary the number of replicas, as well as the number of data points, and the number of replicas over which to enforce the restraints. ---=note-separator=--- They compare ensembles as well in this paper, parameters derived from them. This may be interesting. ---=note-separator=--- This is similar to dynamic ensemble refinement method in that it is also applied to ubq, and S2 and NOE restraints are used. The difference is that here this is a computer experiment where the reference ensemble is obtained using an unrestrained MD. And the S2 and Noe restraints are applied such that all structures in the ensemble are applied S2, whereas pairs of structures are applied the Noe constraints. The authors describe underrestraining and over restraining. Underrestraining occurs when there is not enough restraints. Overrestraining occurs when there are more restraints than the model. When the number of structures in the ensemble increases, whereas the number of restraints remains constant, one gets underrestrained system, or over fit. Overfit b/c more structures than necessary fit to the data. As in curve overfitting. }, doi = {http://dx.doi.org/10.1007/s10858-006-9117-7}, issn = {0925-2738}, journal = {Journal of Biomolecular NMR}, keywords = {ensemble, md, native, nmr, relaxation, structural}, month = {February}, number = {2}, pages = {117--135}, posted-at = {2007-06-01 20:29:20}, priority = {0}, publisher = {Springer}, title = {The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins}, url = {http://dx.doi.org/10.1007/s10858-006-9117-7}, volume = {37}, year = {2007} }

TY - JOUR ID - citeulike:1093615 L3 - citeulike-article-id:1093615 IS - 2 JF - Journal of Biomolecular NMR SN - 0925-2738 EP - 135 TI - The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins PB - Springer VL - 37 SP - 117 KW - ensemble KW - md KW - native KW - nmr KW - relaxation KW - structural N1 - How do they enforce the restraints over pairs or over 16 replicas in the energy function? Do they compute the energy at each step or at the end of each cycle? N1 - They actually do simulated annealing on the replicas, and play with the force constants as well as the temperature in this annealing procedure. They vary the number of replicas, as well as the number of data points, and the number of replicas over which to enforce the restraints. N1 - They compare ensembles as well in this paper, parameters derived from them. This may be interesting. N1 - This is similar to dynamic ensemble refinement method in that it is also applied to ubq, and S2 and NOE restraints are used. The difference is that here this is a computer experiment where the reference ensemble is obtained using an unrestrained MD. And the S2 and Noe restraints are applied such that all structures in the ensemble are applied S2, whereas pairs of structures are applied the Noe constraints. The authors describe underrestraining and over restraining. Underrestraining occurs when there is not enough restraints. Overrestraining occurs when there are more restraints than the model. When the number of structures in the ensemble increases, whereas the number of restraints remains constant, one gets underrestrained system, or over fit. Overfit b/c more structures than necessary fit to the data. As in curve overfitting. AU - Richter AU - Barbara AU - Gsponer AU - Joerg AU - Varnai AU - Peter AU - Salvatella AU - Xavier AU - Vendruscolo AU - Michele PY - 2007/02// UR - http://dx.doi.org/10.1007/s10858-006-9117-7 ER -