Challenges and opportunities in cancer drug resistance

RA Ward, S Fawell, N Floc'h, V Flemington… - Chemical …, 2020 - ACS Publications
There has been huge progress in the discovery of targeted cancer therapies in recent years.
However, even for the most successful and impactful cancer drugs which have been …

Peptide-based electrochemical biosensors utilized for protein detection

V Vanova, K Mitrevska, V Milosavljevic, D Hynek… - Biosensors and …, 2021 - Elsevier
Proteins are generally detected as biomarkers for tracing or determining various disorders in
organisms. Biomarker proteins can be tracked in samples with various origins and in …

DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations

CHM Rodrigues, DEV Pires, DB Ascher - Protein Science, 2021 - Wiley Online Library
Predicting the effect of missense variations on protein stability and dynamics is important for
understanding their role in diseases, and the link between protein structure and function …

mCSM-PPI2: predicting the effects of mutations on protein–protein interactions

CHM Rodrigues, Y Myung, DEV Pires… - Nucleic acids …, 2019 - academic.oup.com
Protein–protein Interactions are involved in most fundamental biological processes, with
disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a …

mmCSM-PPI: predicting the effects of multiple point mutations on protein–protein interactions

CHM Rodrigues, DEV Pires… - Nucleic acids research, 2021 - academic.oup.com
Protein–protein interactions play a crucial role in all cellular functions and biological
processes and mutations leading to their disruption are enriched in many diseases. While a …

mCSM-membrane: predicting the effects of mutations on transmembrane proteins

DEV Pires, CHM Rodrigues… - Nucleic Acids Research, 2020 - academic.oup.com
Significant efforts have been invested into understanding and predicting the molecular
consequences of mutations in protein coding regions, however nearly all approaches have …

[HTML][HTML] Allostery: allosteric cancer drivers and innovative allosteric drugs

R Nussinov, M Zhang, R Maloney, Y Liu, CJ Tsai… - Journal of molecular …, 2022 - Elsevier
Here, we discuss the principles of allosteric activating mutations, propagation downstream of
the signals that they prompt, and allosteric drugs, with examples from the Ras signaling …

epitope3D: a machine learning method for conformational B-cell epitope prediction

BM da Silva, YC Myung, DB Ascher… - Briefings in …, 2022 - academic.oup.com
The ability to identify antigenic determinants of pathogens, or epitopes, is fundamental to
guide rational vaccine development and immunotherapies, which are particularly relevant …

mCSM-AB2: guiding rational antibody design using graph-based signatures

Y Myung, CHM Rodrigues, DB Ascher… - Bioinformatics, 2020 - academic.oup.com
Motivation A lack of accurate computational tools to guide rational mutagenesis has made
affinity maturation a recurrent challenge in antibody (Ab) development. We previously …

mycoCSM: using graph-based signatures to identify safe potent hits against mycobacteria

DEV Pires, DB Ascher - Journal of Chemical Information and …, 2020 - ACS Publications
Development of new potent, safe drugs to treat Mycobacteria has proven to be challenging,
with limited hit rates of initial screens restricting subsequent development efforts. Despite …