@article {Feig2000, title = {Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models}, journal = {Proteins}, volume = {41}, number = {1}, year = {2000}, month = {oct}, pages = {86{\textendash}97}, abstract = {A procedure for the reconstruction of all-atom protein structures from side-chain center-based low-resolution models is introduced and applied to a set of test proteins with high-resolution X-ray structures. The accuracy of the rebuilt all-atom models is measured by root mean square deviations to the corresponding X-ray structures and percentages of correct chi(1) and chi(2) side-chain dihedrals. The benefit of including C(alpha) positions in the low-resolution model is examined, and the effect of lattice-based models on the reconstruction accuracy is discussed. Programs and scripts implementing the reconstruction procedure are made available through the NIH research resource for Multiscale Modeling Tools in Structural Biology (http://mmtsb.scripps.edu).}, keywords = {Models, Molecular, Proteins, Proteins: chemistry}, issn = {0887-3585}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10944396}, author = {M. Feig and Piotr Rotkiewicz and Andrzej Koli{\'n}ski and Jeffrey Skolnick and Charles L. Brooks III} } @article {Vieth1999, title = {Assessing energy functions for flexible docking}, journal = {Journal of Computational Chemistry}, volume = {19}, number = {14}, year = {1999}, pages = {1612{\textendash}1622}, abstract = {A good docking algorithm requires an energy function that is selective, in that it clearly differentiates correctly docked structures from misdocked ones, and that is efficient, meaning that a correctly docked structure can be identified quickly. We assess the selectivity and efficiency of a broad spectrum of energy functions, derived from systematic modifications of the CHARMM param19/toph19 energy function. In particular, we examine the effects of the dielectric constant, the solvation model, the scaling of surface charges, reduction of van der Waals repulsion, and nonbonded cutoffs. Based on an assessment of the energy functions for the docking of five different ligand{\textendash}receptor complexes, we find that selective energy functions include a variety of distance-dependent dielectric models together with truncation of the nonbonded interactions at 8 {\r A}. We evaluate the docking efficiency, the mean number of docked structures per unit of time, of the more selective energy functions, using a simulated annealing molecular dynamics protocol. The largest improvements in efficiency come from a reduction of van der Waals repulsion and a reduction of surface charges. We note that the most selective potential is quite inefficient, although a hierarchical approach can be employed to take advantage of both selective and efficient energy functions.}, keywords = {docking, dynamics, energy functions, Molecular, scoring functions, simulated annealing}, doi = {10.1002/(SICI)1096-987X(19981115)19:14<1612::AID-JCC7>3.0.CO;2-M}, url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(19981115)19:14\%3C1612::AID-JCC7\%3E3.0.CO;2-M/abstract}, author = {Michal Vieth and Jonathan D. Hirst and Andrzej Koli{\'n}ski and Charles L. Brooks III} }