Force Field Validation Using Protein Side Chain Prediction
By Matthew P. Jacobson, George A. Kaminski, Richard A. Friesner, Chaya Rapp. 2002
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
Citations in the corpus
- Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, neutral): “…& Karplus, 1984; Park & Levitt, 1996; Simons et al., 1999), and predicting amino acid sidechain conformations (Bower, Cohen, & Dunbrack, 1997; Jacobson, Kaminski, Friesner, & Rapp, 2002) and free energy changes associated with protein mutations (Gilis & Rooman, 1997; Guerois, Nielsen, &…”
- Energy-based models for atomic-resolution protein conformations (2020, background): “Evaluations of molecular energy functions have used as a measure of fidelity, the ability to identify native side chain configurations (rotamers) from crystal structures where the ground-truth configuration has been masked out (Jacobson et al., 2002; Bower et al., 1997).”
- Force fields for protein simulations. (2003, background): “One important application for protein force fields with highly optimized torsional parameters is the prediction of side-chain rotamer preferences (Jacobson et al., 2002), which is a critical component of accurate protein homology modeling protocols.”
- Recent advances in de novo protein design: Principles, methods, and applications (2021, background): “Scoring functions for soluble proteins take advantage of the large number of solved structures in the PDB to validate and fit the parameters of the score function (121, 122).”
- Toward better refinement of comparative models: Predicting loops in inexact environments (2008, methodology): “The energy is calculated using the Optimized Potential for Liquid Simulations (OPLS) all-atom force field, 21 – 23 the Surface Generalized Born model of polar salvation, 24 an estimator for the nonpolar component of the solvation free energy developed by Gallicchio et al ., 25 and a number of…”
- The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling (2011, methodology): “12–17 These improvements have enabled reasonable results to be obtained for loop predictions up to 20 residues.”
- MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. (2004, methodology): “Several methods are available for the reconstruction of complete all-atom models at moderate levels of accuracy based on C backbones [29–32].”