End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
Relative binding free energy calculations in drug discovery: recent advances and practical considerations
Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …
of structure-based drug design for decades due to the putative value it would bring to the …
The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling
A novel energy model (VSGB 2.0) for high resolution protein structure modeling is
described, which features an optimized implicit solvent model as well as physics‐based …
described, which features an optimized implicit solvent model as well as physics‐based …
[HTML][HTML] Critical assessment of methods for predicting the 3D structure of proteins and protein complexes
SJ Wodak, S Vajda, MF Lensink… - Annual review of …, 2023 - annualreviews.org
Advances in a scientific discipline are often measured by small, incremental steps. In this
review, we report on two intertwined disciplines in the protein structure prediction field …
review, we report on two intertwined disciplines in the protein structure prediction field …
Improved generalized born solvent model parameters for protein simulations
The generalized Born (GB) model is one of the fastest implicit solvent models, and it has
become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with …
become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with …
Molecular enhanced sampling with autoencoders: On‐the‐fly collective variable discovery and accelerated free energy landscape exploration
W Chen, AL Ferguson - Journal of computational chemistry, 2018 - Wiley Online Library
Macromolecular and biomolecular folding landscapes typically contain high free energy
barriers that impede efficient sampling of configurational space by standard molecular …
barriers that impede efficient sampling of configurational space by standard molecular …
Parallel tempering: Theory, applications, and new perspectives
We review the history of the parallel tempering simulation method. From its origins in data
analysis, the parallel tempering method has become a standard workhorse of …
analysis, the parallel tempering method has become a standard workhorse of …
Integrated modeling program, applied chemical theory (IMPACT)
JL Banks, HS Beard, Y Cao, AE Cho… - Journal of …, 2005 - Wiley Online Library
We provide an overview of the IMPACT molecular mechanics program with an emphasis on
recent developments and a description of its current functionality. With respect to core …
recent developments and a description of its current functionality. With respect to core …
The protein folding problem
The “protein folding problem” consists of three closely related puzzles:(a) What is the folding
code?(b) What is the folding mechanism?(c) Can we predict the native structure of a protein …
code?(b) What is the folding mechanism?(c) Can we predict the native structure of a protein …
Molecular dynamics and protein function
M Karplus, J Kuriyan - … of the National Academy of Sciences, 2005 - National Acad Sciences
A fundamental appreciation for how biological macromolecules work requires knowledge of
structure and dynamics. Molecular dynamics simulations provide powerful tools for the …
structure and dynamics. Molecular dynamics simulations provide powerful tools for the …