Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

Using PyMOL as a platform for computational drug design

S Yuan, HCS Chan, Z Hu - Wiley Interdisciplinary Reviews …, 2017 - Wiley Online Library
PyMOL, a cross‐platform molecular graphics tool, has been widely used for three‐
dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron …

Illuminating protein space with a programmable generative model

JB Ingraham, M Baranov, Z Costello, KW Barber… - Nature, 2023 - nature.com
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 …

Antigen-specific antibody design and optimization with diffusion-based generative models for protein structures

S Luo, Y Su, X Peng, S Wang… - Advances in Neural …, 2022 - proceedings.neurips.cc
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 …

ColabFold: making protein folding accessible to all

M Mirdita, K Schütze, Y Moriwaki, L Heo… - Nature …, 2022 - nature.com
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 …

[HTML][HTML] Progen2: exploring the boundaries of protein language models

E Nijkamp, JA Ruffolo, EN Weinstein, N Naik, A Madani - Cell systems, 2023 - cell.com
Attention-based models trained on protein sequences have demonstrated incredible
success at classification and generation tasks relevant for artificial-intelligence-driven …

Accurate prediction of protein structures and interactions using a three-track neural network

M Baek, F DiMaio, I Anishchenko, J Dauparas… - Science, 2021 - science.org
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of
Structure Prediction (CASP14) conference. We explored network architectures that …

Protein structure generation via folding diffusion

KE Wu, KK Yang, R van den Berg, S Alamdari… - Nature …, 2024 - nature.com
The ability to computationally generate novel yet physically foldable protein structures could
lead to new biological discoveries and new treatments targeting yet incurable diseases …

Geometric deep learning of RNA structure

RJL Townshend, S Eismann, AM Watkins, R Rangan… - Science, 2021 - science.org
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 …

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

DE Gordon, GM Jang, M Bouhaddou, J Xu, K Obernier… - Nature, 2020 - nature.com
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 …