Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

By Alexander D. MacKerell, Michael Feig, Charles L. Brooks III. 2004

3,302 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

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

1. Michael Feig
2. Lim Heo
3. David E. Shaw
4. Hahnbeom Park
5. Ron O. Dror
6. Stefano Piana
7. Yang Zhang
8. Chaok Seok

In Molecular Biology

1. Michael Feig
2. Lim Heo
3. David E. Shaw
4. Ron O. Dror
5. Yang Zhang
6. Hahnbeom Park
7. Chaok Seok
8. Torsten Schwede

In Spectroscopy

1. Lim Heo
2. Ron O. Dror
3. Michael Feig
4. Hahnbeom Park
5. Chaok Seok
6. Justin A. Lemkul
7. James C. Gumbart
8. Christophe Chipot

Citations in the corpus

• SWISS-MODEL: homology modelling of protein structures and complexes (2018, positive): “ProMod3 uses the OpenMM library (55) to perform the computations and the CHARMM27 force field (56) for parameterization.”
• Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations (2007, methodology): “All the calculations were performed with CHARMM [28], and the all-atom parameter set PARAM22 for proteins [29] including dihedral cross-term corrections (CMAP) [30] and a modified TIP3P water model [31], as well as recently optimized lipid parameters [32].”
• Systematic Validation of Protein Force Fields against Experimental Data (2012, methodology): “…that our comparison set was comprised of the following eight protein force fields: Amber ff99SB-ILDN [12,14], Amber ff99SB*-ILDN [12–14] Amber ff03 [16], Amber ff03* [13,16], OPLS-AA [17], CHARMM22 [18], CHARMM22 with the CMAP correction ([18,19]; herein termed CHARMM27), and CHARMM22* [15,18,19].”
• Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. (2005, result): “For comparison to both quantum mechanical sampling of the alanine dimer and a survey of the Protein Data Bank, we reference the recent studies of MacKerell et al., which reported grid-based corrections to the (f,c) potential for the CHARMM22 force field (MacKerell et al., 2004a,b).”
• Simulations of interfacial processes: recent advances in force field development (2019, methodology): “Pacella and Gray used IFF and CHARMM22/CMAP FF [13,14] to describe the mineral surfaces, and the peptide was described by Rosetta parameters.”
• Improvements to the APBS biomolecular solvation software suite (2017, methodology): “PDB2PQR currently supports charge/radii force fields from AMBER99 [44], CHARMM22 [45], PARSE [46], PEOE PB [47], Swanson et al.”