Macromolecular modeling and design in Rosetta: recent methods and frameworks
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …
in laboratories worldwide. During two decades of development by a community of …
Using PyMOL as a platform for computational drug design
PyMOL, a cross‐platform molecular graphics tool, has been widely used for three‐
dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron …
dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron …
Illuminating protein space with a programmable generative model
Three billion years of evolution has produced a tremendous diversity of protein molecules,
but the full potential of proteins is likely to be much greater. Accessing this potential has …
but the full potential of proteins is likely to be much greater. Accessing this potential has …
Antigen-specific antibody design and optimization with diffusion-based generative models for protein structures
Antibodies are immune system proteins that protect the host by binding to specific antigens
such as viruses and bacteria. The binding between antibodies and antigens is mainly …
such as viruses and bacteria. The binding between antibodies and antigens is mainly …
ColabFold: making protein folding accessible to all
ColabFold offers accelerated prediction of protein structures and complexes by combining
the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40− 60 …
the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40− 60 …
[HTML][HTML] Progen2: exploring the boundaries of protein language models
Attention-based models trained on protein sequences have demonstrated incredible
success at classification and generation tasks relevant for artificial-intelligence-driven …
success at classification and generation tasks relevant for artificial-intelligence-driven …
Accurate prediction of protein structures and interactions using a three-track neural network
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of
Structure Prediction (CASP14) conference. We explored network architectures that …
Structure Prediction (CASP14) conference. We explored network architectures that …
Protein structure generation via folding diffusion
The ability to computationally generate novel yet physically foldable protein structures could
lead to new biological discoveries and new treatments targeting yet incurable diseases …
lead to new biological discoveries and new treatments targeting yet incurable diseases …
Geometric deep learning of RNA structure
RNA molecules adopt three-dimensional structures that are critical to their function and of
interest in drug discovery. Few RNA structures are known, however, and predicting them …
interest in drug discovery. Few RNA structures are known, however, and predicting them …
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has …
(SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has …