How robust are protein folding simulations with respect to force field parameterization?
By Stefano Piana, K. Lindorff‐Larsen, David E. Shaw. Biophysical Journal, 2011
809 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/bab31fe4850493c8fb20ca2d7944d914691dc75b
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- David E. Shaw
- Stefano Piana
- Ron O. Dror
- David W. Borhani
- Paul Robustelli
- K. Lindorff‐Larsen
- Wouter Boomsma
- Yong Wang
In Molecular Biology
- David E. Shaw
- Stefano Piana
- Ron O. Dror
- David W. Borhani
- Paul Robustelli
- K. Lindorff‐Larsen
- Wouter Boomsma
- Maher M. Kassem
Citations in the corpus
- A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures (2018, background): “may not, in fact, be capable of capturing all relevant sequence-structure effects in a single model (36).”
- Simulations of interfacial processes: recent advances in force field development (2019, methodology): “The interactions between amino acids (or analogs) and graphene are described using the standard combination rules, where the amino acids (or analogs) are represented by CHARMM22* [13,18] non-polarizable”
- Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation. (2016, methodology): “We used the CHARMM22* force field (33) and smoothly shifted the”
- Developing a molecular dynamics force field for both folded and disordered protein states (2018, methodology): “…by previous successful efforts to reparameterize force-field torsion angles to obtain a more accurate balance between helix and coil states (10, 11, 14), we performed a similar torsion optimization targeting (AAQAA) 3 fraction helicity and polyalanine scalar couplings as described previously (14).”