In silico methods and tools for drug discovery

B Shaker, S Ahmad, J Lee, C Jung, D Na - Computers in biology and …, 2021 - Elsevier
In the past, conventional drug discovery strategies have been successfully employed to
develop new drugs, but the process from lead identification to clinical trials takes more than …

Protein assembly by design

J Zhu, N Avakyan, A Kakkis, AM Hoffnagle… - Chemical …, 2021 - ACS Publications
Proteins are nature's primary building blocks for the construction of sophisticated molecular
machines and dynamic materials, ranging from protein complexes such as photosystem II …

Protein complex prediction with AlphaFold-Multimer

R Evans, M O'Neill, A Pritzel, N Antropova, A Senior… - biorxiv, 2021 - biorxiv.org
While the vast majority of well-structured single protein chains can now be predicted to high
accuracy due to the recent AlphaFold model, the prediction of multi-chain protein complexes …

[HTML][HTML] 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] SARS-CoV-2 infection depends on cellular heparan sulfate and ACE2

TM Clausen, DR Sandoval, CB Spliid, J Pihl… - Cell, 2020 - cell.com
We show that SARS-CoV-2 spike protein interacts with both cellular heparan sulfate and
angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD) …

The HDOCK server for integrated protein–protein docking

Y Yan, H Tao, J He, SY Huang - Nature protocols, 2020 - nature.com
Abstract The HDOCK server (http://hdock. phys. hust. edu. cn/) is a highly integrated suite of
homology search, template-based modeling, structure prediction, macromolecular docking …

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

DE Gordon, J Hiatt, M Bouhaddou, VV Rezelj, S Ulferts… - Science, 2020 - science.org
INTRODUCTION The emergence of three lethal coronaviruses in< 20 years and the urgency
of the COVID-19 pandemic have prompted efforts to develop new therapeutic strategies …

[HTML][HTML] A bispecific CAR-T cell therapy targeting BCMA and CD38 in relapsed or refractory multiple myeloma

H Mei, C Li, H Jiang, X Zhao, Z Huang, D Jin… - Journal of Hematology & …, 2021 - Springer
Background BCMA-specific chimeric antigen receptor-T cells (CAR-Ts) have exhibited
remarkable efficacy in refractory or relapsed multiple myeloma (RRMM); however, primary …

Pervasive functional translation of noncanonical human open reading frames

J Chen, AD Brunner, JZ Cogan, JK Nuñez, AP Fields… - Science, 2020 - science.org
Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of
canonical coding sequences (CDSs). In this work, we exploit a systematic CRISPR-based …

[HTML][HTML] The chemistry of snake venom and its medicinal potential

AL Oliveira, MF Viegas, SL da Silva… - Nature Reviews …, 2022 - nature.com
The fascination and fear of snakes dates back to time immemorial, with the first scientific
treatise on snakebite envenoming, the Brooklyn Medical Papyrus, dating from ancient Egypt …