Principles and overview of sampling methods for modeling macromolecular structure and dynamics
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …
how macromolecules carry out their functions in the cell. Significant advances have been …
Computer-aided design of functional protein interactions
Predictive methods for the computational design of proteins search for amino acid
sequences adopting desired structures that perform specific functions. Typically, design …
sequences adopting desired structures that perform specific functions. Typically, design …
Deep geometric representations for modeling effects of mutations on protein-protein binding affinity
Modeling the impact of amino acid mutations on protein-protein interaction plays a crucial
role in protein engineering and drug design. In this study, we develop GeoPPI, a novel …
role in protein engineering and drug design. In this study, we develop GeoPPI, a novel …
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)
The Rosetta molecular modeling software package provides experimentally tested and
rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins …
rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins …
Flex ddG: Rosetta ensemble-based estimation of changes in protein–protein binding affinity upon mutation
Computationally modeling changes in binding free energies upon mutation (interface ΔΔ G)
allows large-scale prediction and perturbation of protein–protein interactions. Additionally …
allows large-scale prediction and perturbation of protein–protein interactions. Additionally …
Regio‐and stereoselective steroid hydroxylation at C7 by cytochrome P450 monooxygenase mutants
Steroidal C7β alcohols and their respective esters have shown significant promise as
neuroprotective and anti‐inflammatory agents to treat chronic neuronal damage like stroke …
neuroprotective and anti‐inflammatory agents to treat chronic neuronal damage like stroke …
AB‐bind: antibody binding mutational database for computational affinity predictions
S Sirin, JR Apgar, EM Bennett, AE Keating - Protein Science, 2016 - Wiley Online Library
Antibodies (Abs) are a crucial component of the immune system and are often used as
diagnostic and therapeutic agents. The need for high‐affinity and high‐specificity antibodies …
diagnostic and therapeutic agents. The need for high‐affinity and high‐specificity antibodies …
Computational design of a modular protein sense-response system
Sensing and responding to signals is a fundamental ability of living systems, but despite
substantial progress in the computational design of new protein structures, there is no …
substantial progress in the computational design of new protein structures, there is no …
Predicting the effect of mutations on protein-protein binding interactions through structure-based interface profiles
The formation of protein-protein complexes is essential for proteins to perform their
physiological functions in the cell. Mutations that prevent the proper formation of the correct …
physiological functions in the cell. Mutations that prevent the proper formation of the correct …
Theoretical and computational protein design
From exponentially large numbers of possible sequences, protein design seeks to identify
the properties of those that fold to predetermined structures and have targeted structural and …
the properties of those that fold to predetermined structures and have targeted structural and …