Protein fragment reconstruction using various modeling techniques

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SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs (2008, methodology): “Structure-based methods can also be used for templatefree modeling [3-6] and model refinement procedures [7, 8].”
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction (2015, methodology): “This approach has been strongly inspired by coarse-grained models developed for protein structure prediction, in particular CABS (15 ) and REFINER (14).”
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. (2012, methodology): “The initial models were subjected to global refinement using SimRNA, a de novo RNA folding method (Rother et al. 2012), which was inspired by the REFINER method for protein folding (Boniecki et al. 2003).”
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement (2012, methodology): “In order to operate, MetaMQAP combines the output from a number of model quality assessment programs (MQAPs), including VERIFY3D [18], PROSA [19], BALA-SNAPP [20], ANO-LEA [21], PROVE [22], TUNE [23], REFINER [24], and PROQRES [25].”
The scoring of poses in protein-protein docking: current capabilities and future directions (2013, unknown): “CP_Qa [159] r”