[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 …

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 …

[HTML][HTML] The structural coverage of the human proteome before and after AlphaFold

E Porta-Pardo, V Ruiz-Serra, S Valentini… - PLoS computational …, 2022 - journals.plos.org
The protein structure field is experiencing a revolution. From the increased throughput of
techniques to determine experimental structures, to developments such as cryo-EM that …

Template-based protein structure modeling using the RaptorX web server

M Källberg, H Wang, S Wang, J Peng, Z Wang, H Lu… - Nature protocols, 2012 - nature.com
A key challenge of modern biology is to uncover the functional role of the protein entities that
compose cellular proteomes. To this end, the availability of reliable three-dimensional …

I-TASSER: a unified platform for automated protein structure and function prediction

A Roy, A Kucukural, Y Zhang - Nature protocols, 2010 - nature.com
The iterative threading assembly refinement (I-TASSER) server is an integrated platform for
automated protein structure and function prediction based on the sequence-to-structure-to …

Machine learning for protein folding and dynamics

F Noé, G De Fabritiis, C Clementi - Current opinion in structural biology, 2020 - Elsevier
Highlights•Advances in machine learning are changing the study of protein folding and
dynamics.•Machine learning is having a large impact in protein structure …

Comparative protein structure modeling using MODELLER

B Webb, A Sali - Current protocols in bioinformatics, 2016 - Wiley Online Library
Comparative protein structure modeling predicts the three‐dimensional structure of a given
protein sequence (target) based primarily on its alignment to one or more proteins of known …

Comparative protein modelling by satisfaction of spatial restraints

A Šali, TL Blundell - Journal of molecular biology, 1993 - Elsevier
We describe a comparative protein modelling method designed to find the most probable
structure for a sequence given its alignment with related structures. The three dimensional …