Recent advances in de novo protein design: Principles, methods, and applications
X Pan, T Kortemme - Journal of Biological Chemistry, 2021 - ASBMB
The computational de novo protein design is increasingly applied to address a number of
key challenges in biomedicine and biological engineering. Successes in expanding …
key challenges in biomedicine and biological engineering. Successes in expanding …
Computational methods in drug discovery
Computer-aided drug discovery/design methods have played a major role in the
development of therapeutically important small molecules for over three decades. These …
development of therapeutically important small molecules for over three decades. These …
[HTML][HTML] CHARMM-GUI supports the Amber force fields
As part of our ongoing efforts to support diverse force fields and simulation programs in
CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber …
CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber …
Accurate de novo design of membrane-traversing macrocycles
We use computational design coupled with experimental characterization to systematically
investigate the design principles for macrocycle membrane permeability and oral …
investigate the design principles for macrocycle membrane permeability and oral …
Protein structure modeling with MODELLER
B Webb, A Sali - Functional genomics: Methods and protocols, 2017 - Springer
Genome sequencing projects have resulted in a rapid increase in the number of known
protein sequences. In contrast, only about one-hundredth of these sequences have been …
protein sequences. In contrast, only about one-hundredth of these sequences have been …
Accurate de novo design of hyperstable constrained peptides
Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks
generally have shapes that have evolved to fit precisely into binding pockets on their targets …
generally have shapes that have evolved to fit precisely into binding pockets on their targets …
GalaxyRefine: Protein structure refinement driven by side-chain repacking
The quality of model structures generated by contemporary protein structure prediction
methods strongly depends on the degree of similarity between the target and available …
methods strongly depends on the degree of similarity between the target and available …
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
We have recently completed a full rearchitecturing of the Rosetta molecular modeling
program, generalizing and expanding its existing functionality. The new architecture enables …
program, generalizing and expanding its existing functionality. The new architecture enables …
GalaxyWEB server for protein structure prediction and refinement
Three-dimensional protein structures provide invaluable information for understanding and
regulating biological functions of proteins. The GalaxyWEB server predicts protein structure …
regulating biological functions of proteins. The GalaxyWEB server predicts protein structure …
CHARMM‐GUI 10 years for biomolecular modeling and simulation
CHARMM‐GUI, http://www. charmm-gui. org, is a web‐based graphical user interface that
prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates …
prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates …