[HTML][HTML] Advances in protein structure prediction and design

B Kuhlman, P Bradley - Nature reviews molecular cell biology, 2019 - nature.com
The prediction of protein three-dimensional structure from amino acid sequence has been a
grand challenge problem in computational biophysics for decades, owing to its intrinsic …

[HTML][HTML] CADD, AI and ML in drug discovery: A comprehensive review

D Vemula, P Jayasurya, V Sushmitha, YN Kumar… - European Journal of …, 2023 - Elsevier
Computer-aided drug design (CADD) is an emerging field that has drawn a lot of interest
because of its potential to expedite and lower the cost of the drug development process …

AlphaFold 2: why it works and its implications for understanding the relationships of protein sequence, structure, and function

J Skolnick, M Gao, H Zhou, S Singh - Journal of chemical …, 2021 - ACS Publications
AlphaFold 2 (AF2) was the star of CASP14, the last biannual structure prediction experiment.
Using novel deep learning, AF2 predicted the structures of many difficult protein targets at or …

AI-based protein structure prediction in drug discovery: impacts and challenges

M Schauperl, RA Denny - Journal of Chemical Information and …, 2022 - ACS Publications
Proteins are the molecular machinery of the human body, and their malfunctioning is often
responsible for diseases, making them crucial targets for drug discovery. The three …

The Rosetta all-atom energy function for macromolecular modeling and design

RF Alford, A Leaver-Fay, JR Jeliazkov… - Journal of chemical …, 2017 - ACS Publications
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse
biological questions and engineering challenges ranging from interpretation of low …

[HTML][HTML] Computational methods in drug discovery

SP Leelananda, S Lindert - Beilstein journal of organic …, 2016 - beilstein-journals.org
The process for drug discovery and development is challenging, time consuming and
expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut …

Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks

MP Hughes, MR Sawaya, DR Boyer, L Goldschmidt… - Science, 2018 - science.org
Subcellular membraneless assemblies are a reinvigorated area of study in biology, with
spirited scientific discussions on the forces between the low-complexity protein domains …

A brief history of de novo protein design: minimal, rational, and computational

DN Woolfson - Journal of Molecular Biology, 2021 - Elsevier
Protein design has come of age, but how will it mature? In the 1980s and the 1990s, the
primary motivation for de novo protein design was to test our understanding of the …

Toward the solution of the protein structure prediction problem

R Pearce, Y Zhang - Journal of Biological Chemistry, 2021 - ASBMB
Since Anfinsen demonstrated that the information encoded in a protein's amino acid
sequence determines its structure in 1973, solving the protein structure prediction problem …

Deep‐learning contact‐map guided protein structure prediction in CASP13

W Zheng, Y Li, C Zhang, R Pearce… - Proteins: Structure …, 2019 - Wiley Online Library
We report the results of two fully automated structure prediction pipelines,“Zhang‐Server”
and “QUARK”, in CASP13. The pipelines were built upon the C‐I‐TASSER and C‐QUARK …