Semiempirical quantum mechanical methods for noncovalent interactions for chemical and biochemical applications
Semiempirical (SE) methods can be derived from either Hartree–Fock or density functional
theory by applying systematic approximations, leading to efficient computational schemes …
theory by applying systematic approximations, leading to efficient computational schemes …
Biophysical experiments and biomolecular simulations: A perfect match?
S Bottaro, K Lindorff-Larsen - Science, 2018 - science.org
A fundamental challenge in biological research is achieving an atomic-level description and
mechanistic understanding of the function of biomolecules. Techniques for biomolecular …
mechanistic understanding of the function of biomolecules. Techniques for biomolecular …
ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution
Molecular dynamics (MD) simulations have become increasingly popular in studying the
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …
Developing a molecular dynamics force field for both folded and disordered protein states
Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural
dynamics of folded proteins and should be similarly applicable to disordered proteins and …
dynamics of folded proteins and should be similarly applicable to disordered proteins and …
ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB
JA Maier, C Martinez, K Kasavajhala… - Journal of chemical …, 2015 - ACS Publications
Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force
field is required. The Amber ff99SB force field improved protein secondary structure balance …
field is required. The Amber ff99SB force field improved protein secondary structure balance …
Improved peptide and protein torsional energetics with the OPLS-AA force field
MJ Robertson, J Tirado-Rives… - Journal of chemical …, 2015 - ACS Publications
The development and validation of new peptide dihedral parameters are reported for the
OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1 …
OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1 …
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
While the quality of the current CHARMM22/CMAP additive force field for proteins has been
demonstrated in a large number of applications, limitations in the model with respect to the …
demonstrated in a large number of applications, limitations in the model with respect to the …
Balanced protein–water interactions improve properties of disordered proteins and non-specific protein association
Some frequently encountered deficiencies in all-atom molecular simulations, such as
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
Polarizable atomic multipole-based AMOEBA force field for proteins
Development of the AMOEBA (atomic multipole optimized energetics for biomolecular
simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes …
simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes …
Polyproline-II helix in proteins: structure and function
AA Adzhubei, MJE Sternberg, AA Makarov - Journal of molecular biology, 2013 - Elsevier
The poly-l-proline type II (PPII) helix in recent years has emerged clearly as a structural class
not only of fibrillar proteins (in collagen, PPII is a dominant conformation) but also of the …
not only of fibrillar proteins (in collagen, PPII is a dominant conformation) but also of the …