[HTML][HTML] Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health

HC Jubb, AP Pandurangan, MA Turner… - Progress in biophysics …, 2017 - Elsevier
Many essential biological processes including cell regulation and signalling are mediated
through the assembly of protein complexes. Changes to protein-protein interaction (PPI) …

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 …

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

CHM Rodrigues, DEV Pires… - Nucleic acids research, 2018 - academic.oup.com
Proteins are highly dynamic molecules, whose function is intrinsically linked to their
molecular motions. Despite the pivotal role of protein dynamics, their computational …

Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures

Q Pan, TB Nguyen, DB Ascher… - Briefings in …, 2022 - academic.oup.com
Abstract Changes in protein sequence can have dramatic effects on how proteins fold, their
stability and dynamics. Over the last 20 years, pioneering methods have been developed to …

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 …

SDM: a server for predicting effects of mutations on protein stability

AP Pandurangan, B Ochoa-Montano… - Nucleic acids …, 2017 - academic.oup.com
Here, we report a webserver for the improved SDM, used for predicting the effects of
mutations on protein stability. As a pioneering knowledge-based approach, SDM has been …

[HTML][HTML] Arpeggio: a web server for calculating and visualising interatomic interactions in protein structures

HC Jubb, AP Higueruelo, B Ochoa-Montaño… - Journal of molecular …, 2017 - Elsevier
Interactions between proteins and their ligands, such as small molecules, other proteins,
and DNA, depend on specific interatomic interactions that can be classified on the basis of …

pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures

DEV Pires, TL Blundell, DB Ascher - Journal of medicinal …, 2015 - ACS Publications
Drug development has a high attrition rate, with poor pharmacokinetic and safety properties
a significant hurdle. Computational approaches may help minimize these risks. We have …

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

KE Holt, P McAdam, PVK Thai, NTT Thuong, DTM Ha… - Nature …, 2018 - nature.com
To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from
tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of …

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 …