The protein corona from nanomedicine to environmental science

M Mahmoudi, MP Landry, A Moore… - Nature Reviews Materials, 2023 - nature.com
The protein corona spontaneously develops and evolves on the surface of nanoscale
materials when they are exposed to biological environments, altering their physiochemical …

AI-powered therapeutic target discovery

FW Pun, IV Ozerov, A Zhavoronkov - Trends in pharmacological sciences, 2023 - cell.com
Disease modeling and target identification are the most crucial initial steps in drug
discovery, and influence the probability of success at every step of drug development …

UCSF ChimeraX: Tools for structure building and analysis

EC Meng, TD Goddard, EF Pettersen… - Protein …, 2023 - Wiley Online Library
Advances in computational tools for atomic model building are leading to accurate models of
large molecular assemblies seen in electron microscopy, often at challenging resolutions of …

Accurate proteome-wide missense variant effect prediction with AlphaMissense

J Cheng, G Novati, J Pan, C Bycroft, A Žemgulytė… - Science, 2023 - science.org
The vast majority of missense variants observed in the human genome are of unknown
clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on …

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

R Krishna, J Wang, W Ahern, P Sturmfels, P Venkatesh… - Science, 2024 - science.org
Deep-learning methods have revolutionized protein structure prediction and design but are
presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which …

The CCP4 suite: integrative software for macromolecular crystallography

J Agirre, M Atanasova, H Bagdonas… - Biological …, 2023 - journals.iucr.org
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective
with a mission to develop, test, distribute and promote software for macromolecular …

Predicting multiple conformations via sequence clustering and AlphaFold2

HK Wayment-Steele, A Ojoawo, R Otten, JM Apitz… - Nature, 2024 - nature.com
Abstract AlphaFold2 (ref.) has revolutionized structural biology by accurately predicting
single structures of proteins. However, a protein's biological function often depends on …

RCSB Protein Data Bank (RCSB. org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from …

SK Burley, C Bhikadiya, C Bi, S Bittrich… - Nucleic acids …, 2023 - academic.oup.com
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB
PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center …

InterPro in 2022

T Paysan-Lafosse, M Blum, S Chuguransky… - Nucleic acids …, 2023 - academic.oup.com
Abstract The InterPro database (https://www. ebi. ac. uk/interpro/) provides an integrative
classification of protein sequences into families, and identifies functionally important …

SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina

M Bugnon, UF Röhrig, M Goullieux… - Nucleic acids …, 2024 - academic.oup.com
Drug discovery aims to identify potential therapeutic compounds capable of modulating the
activity of specific biological targets. Molecular docking can efficiently support this process …