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Scalable molecular dynamics on CPU and GPU architectures with NAMD.
- James C. Phillips, David J. Hardy, E. Tajkhorshid
- Computer ScienceThe Journal of chemical physics
- 28 July 2020
The main features of NAMD are reviewed, including the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and their applicability to specific problems.
Enhanced sampling techniques in molecular dynamics simulations of biological systems.
NAMD goes quantum: An integrative suite for QM/MM simulations
By combining the widely used molecular dynamics and visualization programs NAMD and VMD with the quantum chemistry packages ORCA and MOPAC, this work has created an integrated, comprehensive, customizable, and easy-to-use suite.
Direction Matters: Monovalent Streptavidin/Biotin Complex under Load.
Interestingly, it is observed that depending on force loading geometry, partial unfolding of N-terminal region of monovalent streptavidin occurs before biotin is released from the binding pocket.
Mining for encrypted peptide antibiotics in the human proteome
- M. D. Torres, Marcelo C. R. Melo, O. Crescenzi, E. Notomista, C. de la Fuente-Nunez
- BiologyNature biomedical engineering
- 4 November 2021
It is shown that the encrypted peptides kill pathogenic bacteria by targeting their membrane, modulate gut and skin commensals, do not readily select for bacterial resistance, and possess anti-infective activity in skin abscess and thigh infection mouse models.
Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories.
- Marcelo C. R. Melo, R. C. Bernardi, C. de la Fuente-Nunez, Z. Luthey-Schulten
- Biology, ChemistryThe Journal of chemical physics
- 1 October 2020
The enhanced and updated protocol provides the community with an intuitive and interactive interface, which can be easily applied to large macromolecular complexes, and is employed to investigate three different systems, with up to 2.5M atoms.
Fundamental behaviors emerge from simulations of a living minimal cell
Population FBA predicts metabolic phenotypes in yeast
- Piyush Labhsetwar, Marcelo C. R. Melo, John A. Cole, Z. Luthey-Schulten
- BiologyPLoS Comput. Biol.
- 1 September 2017
The partitioning of flux between fermentation and respiration predicted by the Population FBA model agrees with recent 13C fluxomics experiments, and the Crabtree effect is largely recovered, while FBA without proteomics constraints predicts respirative metabolism almost exclusively.
Accelerating antibiotic discovery through artificial intelligence
- Marcelo C. R. Melo, Jacqueline R. M. A. Maasch, C. de la Fuente-Nunez
- BiologyCommunications biology
- 9 September 2021
This review describes AI-facilitated advances in the discovery of both small molecule antibiotics and antimicrobial peptides and analyzes uptake of open science best practices in AI-driven antibiotic discovery and argues for openness and reproducibility as a means of accelerating preclinical research.
Kinetic Modeling of the Genetic Information Processes in a Minimal Cell
JCVI-syn3A is a minimal bacterial cell with a 543 kbp genome consisting of 493 genes. For this slow growing minimal cell with a 105 min doubling time, we recently established the essential metabolism…