Birth and future of multiscale modeling for macromolecular systems (Nobel Lecture)
M Levitt - Angewandte Chemie International Edition, 2014 - Wiley Online Library
Winning the Nobel Prize is a unique and marvelous experience that no one can prepare for
or in any way know what to expect. The instantaneous transformation from an ordinary …
or in any way know what to expect. The instantaneous transformation from an ordinary …
Avoiding false positive conclusions in molecular simulation: the importance of replicas
Molecular simulations are a computational technique used to investigate the dynamics of
proteins and other molecules. The free energy landscape of these simulations is often …
proteins and other molecules. The free energy landscape of these simulations is often …
Modeling nucleic acids
Nucleic acids are an important class of biological macromolecules that carry out a variety of
cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold …
cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold …
Tuning cytokine receptor signaling by re-orienting dimer geometry with surrogate ligands
Most cell-surface receptors for cytokines and growth factors signal as dimers, but it is unclear
whether remodeling receptor dimer topology is a viable strategy to" tune" signaling output …
whether remodeling receptor dimer topology is a viable strategy to" tune" signaling output …
Computational design of structured loops for new protein functions
The ability to engineer the precise geometries, fine-tuned energetics and subtle dynamics
that are characteristic of functional proteins is a major unsolved challenge in the field of …
that are characteristic of functional proteins is a major unsolved challenge in the field of …
Structural and mechanistic insight into DNA bending by antitumour calicheamicins
A Mills, F Gago - Organic & Biomolecular Chemistry, 2021 - pubs.rsc.org
Among the class of enediyne antibiotics endowed with potent antitumour activities, the
calicheamicin derivative known as ozogamicin is selectively targeted to several leukaemia …
calicheamicin derivative known as ozogamicin is selectively targeted to several leukaemia …
Random coordinate descent with spinor-matrices and geometric filters for efficient loop closure
P Chys, P Chacón - Journal of chemical theory and computation, 2013 - ACS Publications
Protein loop closure constitutes a critical step in loop and protein modeling whereby
geometrically feasible loops must be found between two given anchor residues. Here, a new …
geometrically feasible loops must be found between two given anchor residues. Here, a new …
Modeling and design by hierarchical natural moves
We develop a unique algorithm implemented in the program MOSAICS (Methodologies for
Optimization and Sampling in Computational Studies) that is capable of nanoscale modeling …
Optimization and Sampling in Computational Studies) that is capable of nanoscale modeling …
Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images
The method presented here refines molecular conformations directly against projections of
single particles measured by electron microscopy. By optimizing the orientation of the …
single particles measured by electron microscopy. By optimizing the orientation of the …
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo
Motivation: The binding between a peptide and a major histocompatibility complex (MHC) is
one of the most important processes for the induction of an adaptive immune response …
one of the most important processes for the induction of an adaptive immune response …