Explanipedia

Circulating microRNA profiles are associated with acute pain and stress in castrated and tail docked lambs Open

Ryan J. Farr, Christopher Cowled, Carlos H. M. Rodrigues, Christina L. Rootes, Dana L. M. Campbell , et al. · 2025

Proximity proteomics reveals a mechanism of fatty acid transfer at lipid droplet-mitochondria- endoplasmic reticulum contact sites Open

Ayenachew Bezawork‐Geleta, Camille J. Devereux, Stacey N. Keenan, Jieqiong Lou, Hyun‐Jung Cho , et al. · 2025

Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges Open

Paola Turina, Maria Petrosino, Carlos A. Enriquez Sandoval, Leonore Novak, Alessandra Pasquo , et al. · 2025

Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges Open

Paola Turina, Giuditta Dal Cortivo, Carlos A. Enriquez Sandoval, Emil Alexov, David B. Ascher , et al. · 2024

piscesCSM: prediction of anticancer synergistic drug combinations Open

Raghad Al‐Jarf, Carlos H. M. Rodrigues, Yoochan Myung, Douglas E. V. Pires, David B. Ascher · 2024

While drug combination therapies are of great importance, particularly in cancer treatment, identifying novel synergistic drug combinations has been a challenging venture. Computational methods have emerged in this context as a promising t…

MTR3D‐AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2 Open

Aaron S. Kovacs, Stephanie Portelli, Michael Silk, Carlos H. M. Rodrigues, David B. Ascher · 2024

The missense tolerance ratio (MTR) was developed as a novel approach to assess the deleteriousness of variants. Its three‐dimensional successor, MTR3D, was demonstrated powerful at discriminating pathogenic from benign variants. However, i…

EFG‐CS: Predicting chemical shifts from amino acid sequences with protein structure prediction using machine learning and deep learning models Open

Xiaotong Gu, Yoochan Myung, Carlos H. M. Rodrigues, David B. Ascher · 2024

Nuclear magnetic resonance (NMR) crystallography is one of the main methods in structural biology for analyzing protein stereochemistry and structure. The chemical shift of the resonance frequency reflects the effect of the protons in a mo…

DDMut-PPI: predicting effects of mutations on protein–protein interactions using graph-based deep learning Open

Yunzhuo Zhou, Yoochan Myung, Carlos H. M. Rodrigues, David B. Ascher · 2024

Protein–protein interactions (PPIs) play a vital role in cellular functions and are essential for therapeutic development and understanding diseases. However, current predictive tools often struggle to balance efficiency and precision in p…

Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges Open

Carlos H. M. Rodrigues, Stephanie Portelli, David B. Ascher · 2024

CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces Open

Carlos H. M. Rodrigues, David B. Ascher · 2023

Proteins are molecular machinery that participate in virtually all essential biological functions within the cell, which are tightly related to their 3D structure. The importance of understanding protein structure–function relationship is …

LEGO-CSM: a tool for functional characterization of proteins Open

Thanh Nguyen, Alex G. C. de Sá, Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher · 2023

Motivation With the development of sequencing techniques, the discovery of new proteins significantly exceeds the human capacity and resources for experimentally characterizing protein functions. Localization, EC numbers, and GO terms with…

DDMut: predicting effects of mutations on protein stability using deep learning Open

Yunzhuo Zhou, Qisheng Pan, Douglas E. V. Pires, Carlos H. M. Rodrigues, David B. Ascher · 2023

Understanding the effects of mutations on protein stability is crucial for variant interpretation and prioritisation, protein engineering, and biotechnology. Despite significant efforts, community assessments of predictive tools have highl…

CSM-Toxin: A Web-Server for Predicting Protein Toxicity Open

Vladimir Morozov, Carlos H. M. Rodrigues, David B. Ascher · 2023

Biologics are one of the most rapidly expanding classes of therapeutics, but can be associated with a range of toxic properties. In small-molecule drug development, early identification of potential toxicity led to a significant reduction …

DockNet: high-throughput protein–protein interface contact prediction Open

Nathan P. Williams, Carlos H. M. Rodrigues, Jia Q. Truong, David B. Ascher, Jessica K. Holien · 2022

Motivation Over 300 000 protein–protein interaction (PPI) pairs have been identified in the human proteome and targeting these is fast becoming the next frontier in drug design. Predicting PPI sites, however, is a challenging task that tra…

A structural biology community assessment of AlphaFold2 applications Open

Mehmet Akdel, Douglas E. V. Pires, Eduard Porta‐Pardo, Jürgen Jänes, Arthur O. Zalevsky , et al. · 2022

kinCSM: Using graph‐based signatures to predict small molecule CDK2 inhibitors Open

Yunzhuo Zhou, Raghad Al‐Jarf, Azadeh Alavi, Thanh Nguyen, Carlos H. M. Rodrigues , et al. · 2022

Protein phosphorylation acts as an essential on/off switch in many cellular signaling pathways. This has led to ongoing interest in targeting kinases for therapeutic intervention. Computer‐aided drug discovery has been proven a useful and …

CSM‐peptides: A computational approach to rapid identification of therapeutic peptides Open

Carlos H. M. Rodrigues, Anjali Garg, David W. Keizer, Douglas E. V. Pires, David B. Ascher · 2022

Peptides are attractive alternatives for the development of new therapeutic strategies due to their versatility and low complexity of synthesis. Increasing interest in these molecules has led to the creation of large collections of experim…

CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning Open

Carlos H. M. Rodrigues, David B. Ascher · 2022

Recent advances in protein structural modelling have enabled the accurate prediction of the holo 3D structures of almost any protein, however protein function is intrinsically linked to the interactions it makes. While a number of computat…

Structural landscapes of PPI interfaces Open

Carlos H. M. Rodrigues, Douglas E. V. Pires, Tom L. Blundell, David B. Ascher · 2022

Proteins are capable of highly specific interactions and are responsible for a wide range of functions, making them attractive in the pursuit of new therapeutic options. Previous studies focusing on overall geometry of protein–protein inte…

Applying Sodium Carbonate Extraction Mass Spectrometry to Investigate Defects in the Mitochondrial Respiratory Chain Open

David R. L. Robinson, Daniella H. Hock, Linden Muellner-Wong, Roopasingam Kugapreethan, Boris Reljić , et al. · 2022

Mitochondria are complex organelles containing 13 proteins encoded by mitochondrial DNA and over 1,000 proteins encoded on nuclear DNA. Many mitochondrial proteins are associated with the inner or outer mitochondrial membranes, either peri…

HGDiscovery: An online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase Open

Malancha Karmakar, Vittoria Cicaloni, Carlos H. M. Rodrigues, Ottavia Spiga, Annalisa Santucci , et al. · 2022

A structural biology community assessment of AlphaFold 2 applications Open

Mehmet Akdel, Douglas E. V. Pires, Eduard Porta‐Pardo, Jürgen Jänes, Arthur O. Zalevsky , et al. · 2021

Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods have led to protein structure predictions that have reached the accur…

kinCSM: using graph-based signatures to predict small molecule CDK2 kinase inhibitors Open

Yunzhuo Zhou, Raghad Al‐Jarf, Azadeh Alavi, Thanh Nguyen, Carlos H. M. Rodrigues , et al. · 2021

Protein phosphorylation acts as an essential on/off switch in many cellular signalling pathways, regulating protein function. This has led to ongoing interest in targeting kinases for therapeutic intervention. Computer-aided drug discovery…

MTR3D: identifying regions within protein tertiary structures under purifying selection Open

Michael Silk, Douglas E. V. Pires, Carlos H. M. Rodrigues, Elston N. D’Souza, Moshe Olshansky , et al. · 2021

The identification of disease-causal variants is non-trivial. By mapping population variation from over 448,000 exome and genome sequences to over 81,000 experimental structures and homology models of the human proteome, we have calculated…

HGDiscovery: an online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase Open

Malancha Karmakar, Vittoria Cicaloni, Carlos H. M. Rodrigues, Ottavia Spiga, Annalisa Santucci , et al. · 2021

Alkaptonuria (AKU), a rare genetic disorder, is characterized by the accumulation of homogentisic acid (HGA) in the body. Affected individuals lack enough functional levels of an enzyme required to breakdown HGA. Mutations in the HGD gene …

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

Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher · 2021

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 number of computational methods to assess the effects of v…

Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource Open

Stephanie Portelli, Moshe Olshansky, Carlos H. M. Rodrigues, Elston N. D’Souza, Yoochan Myung , et al. · 2021

Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase Open

Yunzhuo Zhou, Stephanie Portelli, Megan Pat, Carlos H. M. Rodrigues, Thanh Nguyen , et al. · 2021

Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource Open

Stephanie Portelli, Moshe Olshansky, Carlos H. M. Rodrigues, Elston N. D’Souza, Yoochan Myung , et al. · 2020

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

Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher · 2020

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. Approaches to estimate these changes have been propo…

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