2026· Methods in molecular biology· Vol 3043, pp.
115-134
· 0 citations
Medicine
TL;DR
This chapter presents a practical, end-to-end protocol for performing MD simulations on large biomolecules, using a full-length antibody as a case study and introduces foundational software tools commonly used in molecular modeling and MD simulations, including PyMOL, visual molecular dynamics (VMD), nanoscale molecular dynamics (NAMD), MDAnalysis, and others.
A practical overview of classical atomistic MD methodologies commonly used in medicinal chemistry, including force-field-based simulations, enhanced sampling techniques, and free-energy calculation methods such as alchemical and end-point approaches are provided.
S. S. Çınaroğlu· Mini-Reviews in Medical Chem...· 1 citation
Classical molecular dynamics is a theoretical method useful for investigating noncovalent intermolecular interactions and conformational flexibility, enabling the simulation of processes such as aggregation/dissolution and adsorption. Molecular dynamics and quantum chemistry are increasingly introduced in chemistry c...
C. Picarelli, G. Raffaini, M. Tommasini· Journal of Chemical Educatio...· 0 citations
Protein–protein interactions are stochastic and play a central role in determining the structural and dynamic properties of biological systems. Computational approaches that account for the probabilistic nature of these interactions are therefore essential for understanding processes ranging from molecular self-assem...
L. D. de Oliveira, Luiz Fernando de Camargo Rodrigues, R. Itri· Biophysical Reviews· 0 citations
An improved force field is developed, derived from its parent, Amber ff24EXP-GA, and its evaluation against Amber ff14SB and other contemporary force fields, such as CHARMM36m, in capturing the empirically determined conformational properties of unfolded systems: short peptides that serve as model systems for IDPs, and...
The theoretical, computational and cultural challenges that need to be overcome to gain an understanding of the biological mesoscale are described and potential solutions are offered.
Sarah Harris, Gianluca Lattanzi, Angelo Rosa et al.· Biophysical Journal· 0 citations
It is demonstrated that BioEmu can generate plausible conformational ensembles for relatively large, six-and seven-pass membrane proteins, sampling rare states at a fraction of the computational cost of conventional MD simulations, suggesting that AI-based ensemble generation could provide an accessible approach for ex...
B. Clifton, Adam G. Grieve, Robin A. Corey· bioRxiv· 0 citations
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