A critical assessment of comparative molecular modeling of tertiary structures of proteins *

By S. Mosimann, Ron Meleshko, M. James. 1995

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Citations in the corpus

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests (2013, methodology): “…prediction techniques: In the first installments of CASP, root-mean-square deviation (RMSD) between a prediction and the superposed reference structures was used in various forms as the main evaluation criterion (Hubbard, 1999; Jones and Kleywegt, 1999; Martin et al., 1997; Mosimann et al., 1995).”
ESyPred3D: Prediction of proteins 3D structures (2002, background): “Among these critical steps, it is commonly accepted that the target–template alignment step is the most critical ( Mosimann et al., 1995; Martin et al., 1997).”
Evaluation of template-based models in CASP8 with standard measures (2009, methodology): “The root mean square deviation (RMSD) was the metric used in CASP1-32–4 and its use is still very widespread among computational biologists due to its conceptual simplicity.”
RMS/Coverage graphs: A qualitative method for comparing three‐dimensional protein structure predictions (1999, methodology): “The information shown is: (1) prediction ID; (2) predictor group; (3) number of predictions; (4) the number of residues predicted; (5) an RMS; (6) links labeled [p], [i], [s]; (7) the identifier of the PDB chain from which the model is predicted; (8) the SCOP fold code for the PDB code; and (9) the ”
Assessing protein structures with a non-local atomic interaction energy. (1998, methodology): “The NL-pro®les were calculated for the X-ray solved protein and for the best models (Mosimann et al., 1995).”
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. (1998, methodology): “MISFOLD 25 8.66‐22.43 (Braxenthaler et al., 1997; Holm & Sander, 1992b) CASPI 42 0.53‐7.40 ( Mosimann et al., 1995; Braxenthaler et al., 1997) IFU 44 0.21‐10.02 (Braxenthaler et al., 1997; Pedersen & Moult, 1997) PDBERR 3 0.81‐13.21 (Braxenthaler et al., 1997) SGPA 2 1.91‐2.06 (Braxenthaler et al.,”
Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction (2002, background): “Thus, indeed, 1.57 produces the most accurate potential.”