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 …

Avoiding false positive conclusions in molecular simulation: the importance of replicas

B Knapp, L Ospina, CM Deane - Journal of Chemical Theory and …, 2018 - ACS Publications
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 …

Modeling nucleic acids

AYL Sim, P Minary, M Levitt - Current opinion in structural biology, 2012 - Elsevier
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 …

Tuning cytokine receptor signaling by re-orienting dimer geometry with surrogate ligands

I Moraga, G Wernig, S Wilmes, V Gryshkova… - Cell, 2015 - cell.com
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 …

Computational design of structured loops for new protein functions

K Kundert, T Kortemme - Biological chemistry, 2019 - degruyter.com
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 …

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 …

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 …

Modeling and design by hierarchical natural moves

AYL Sim, M Levitt, P Minary - Proceedings of the National …, 2012 - National Acad Sciences
We develop a unique algorithm implemented in the program MOSAICS (Methodologies for
Optimization and Sampling in Computational Studies) that is capable of nanoscale modeling …

Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images

J Zhang, P Minary, M Levitt - Proceedings of the National …, 2012 - National Acad Sciences
The method presented here refines molecular conformations directly against projections of
single particles measured by electron microscopy. By optimizing the orientation of the …

Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo

B Knapp, S Demharter, CM Deane, P Minary - Bioinformatics, 2016 - academic.oup.com
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 …