Riccardo Pellarin
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View article: Kinetic principles of chemical cross-link formation for protein–protein interactions
Kinetic principles of chemical cross-link formation for protein–protein interactions Open
Proteins play a central role in most biological processes within the cell, and deciphering how they interact is key to understand their function. Cross-linking coupled with mass spectrometry is an essential tool for elucidating protein–pro…
View article: Kinetic principles of chemical cross-link formation for protein-protein interactions
Kinetic principles of chemical cross-link formation for protein-protein interactions Open
Proteins play a central role in most biological processes within the cell and deciphering how they interact is key to understand their function. Cross-linking coupled to mass spectrometry is an essential tool for elucidating protein-protei…
View article: AlignScape, displaying sequence similarity using self-organizing maps
AlignScape, displaying sequence similarity using self-organizing maps Open
The current richness of sequence data needs efficient methodologies to display and analyze the complexity of the information in a compact and readable manner. Traditionally, phylogenetic trees and sequence similarity networks have been use…
View article: Front Cover: Interrogating Aptamer Chemical Space Through Modified Nucleotide Substitution Facilitated by Enzymatic DNA Synthesis (ChemBioChem 1/2024)
Front Cover: Interrogating Aptamer Chemical Space Through Modified Nucleotide Substitution Facilitated by Enzymatic DNA Synthesis (ChemBioChem 1/2024) Open
Chemically modified aptamers are typically obtained through SELEX with unnatural nucleotides. If binding affinity or specificity falls short, re-selection or post-SELEX methods that are often time-consuming or synthetically challenging bec…
View article: Rational Prediction of PROTAC-Compatible Protein–Protein Interfaces by Molecular Docking
Rational Prediction of PROTAC-Compatible Protein–Protein Interfaces by Molecular Docking Open
Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose interaction with the ubiquitination machinery leads to ta…
View article: Interrogating Aptamer Chemical Space Through Modified Nucleotide Substitution Facilitated by Enzymatic DNA Synthesis
Interrogating Aptamer Chemical Space Through Modified Nucleotide Substitution Facilitated by Enzymatic DNA Synthesis Open
Chemical modification of aptamers is an important step to improve their performance and stability in biological media. This can be performed either during their identification (mod‐SELEX) or after the in vitro selection process (post‐SELEX…
View article: Acinetobacter type VI secretion system comprises a non-canonical membrane complex
Acinetobacter type VI secretion system comprises a non-canonical membrane complex Open
A . baumannii can rapidly acquire new resistance mechanisms and persist on abiotic surface, enabling the colonization of asymptomatic human host. In Acinetobacter the type VI secretion system (T6SS) is involved in twitching, surface motili…
View article: Data_for_Rational_Prediction_of_PROTAC_Compatible_PPI
Data_for_Rational_Prediction_of_PROTAC_Compatible_PPI Open
Tar file containing the dataset used for the "Rational prediction of PROTAC compatible ligase-target interfaces" manuscript by Pereira et al.
View article: Data_for_Rational_Prediction_of_PROTAC_Compatible_PPI
Data_for_Rational_Prediction_of_PROTAC_Compatible_PPI Open
Tar file containing the dataset used for the "Rational prediction of PROTAC compatible ligase-target interfaces" manuscript by Pereira et al.
View article: Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking
Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking Open
Proteolysis targeting chimeras (PROTACS) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex whose interaction with the ubiquitination machinery leads to tar…
View article: Mono- and Intralink Filter (Mi-Filter) To Reduce False Identifications in Cross-Linking Mass Spectrometry Data
Mono- and Intralink Filter (Mi-Filter) To Reduce False Identifications in Cross-Linking Mass Spectrometry Data Open
Cross-linking mass spectrometry (XL-MS) has become an indispensable tool for the emerging field of systems structural biology over the recent years. However, the confidence in individual protein-protein interactions (PPIs) depends on the c…
View article: Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution
Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution Open
Electron cryo-microscopy (cryo-EM) has emerged as a powerful method by which to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-…
View article: Inhibiting Type VI Secretion System Activity with a Biomimetic Peptide Designed To Target the Baseplate Wedge Complex
Inhibiting Type VI Secretion System Activity with a Biomimetic Peptide Designed To Target the Baseplate Wedge Complex Open
New therapeutic options are urgently needed to fight drug-resistant and life-threatening infections. In contrast to antibiotics that inhibit the growth pathways of bacteria, the antivirulence strategy is a promising approach to disarm path…
View article: Genetic interaction mapping informs integrative structure determination of protein complexes
Genetic interaction mapping informs integrative structure determination of protein complexes Open
From phenotype to structure Much insight has come from structures of macromolecular complexes determined by methods such as crystallography or cryo–electron microscopy. However, looking at transient complexes remains challenging, as does d…
View article: Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution
Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution Open
Electron cryo-microscopy (cryo-EM) has emerged as a powerful method to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-atomic re…
View article: RNA Pol III input data and output models
RNA Pol III input data and output models Open
This repository contains the input experimental data used in a tutorial on modeling of RNA Polymerase III and the largest cluster of output models.
View article: RNA Pol III input data and output models
RNA Pol III input data and output models Open
This repository contains the input experimental data used in a tutorial on modeling of RNA Polymerase III and the largest cluster of output models.
View article: RNA Pol III input data and output models
RNA Pol III input data and output models Open
This repository contains the input experimental data used in a tutorial on modeling of RNA Polymerase III and the largest cluster of output models.
View article: Pol III modeling data and scripts using the Integrative Modeling Platform
Pol III modeling data and scripts using the Integrative Modeling Platform Open
This repository contains the data obtained running the Integrative modeling platform with crosslinks and cryoem data, on the RNA Pol III system.
View article: Pol III modeling data and scripts using the Integrative Modeling Platform
Pol III modeling data and scripts using the Integrative Modeling Platform Open
This repository contains the data obtained running the Integrative modeling platform with crosslinks and cryoem data, on the RNA Pol III system.
View article: Pol III modeling data and scripts using the Integrative Modeling Platform
Pol III modeling data and scripts using the Integrative Modeling Platform Open
This repository contains the data obtained running the Integrative modeling platform with crosslinks and cryoem data, on the RNA Pol III system.
View article: Role of integrative structural biology in understanding transcriptional initiation
Role of integrative structural biology in understanding transcriptional initiation Open
Integrative structural biology combines data from multiple experimental techniques to generate complete structural models for the biological system of interest. Most commonly cross-linking data sets are employed alongside electron microsco…
View article: <i>In situ</i> and high-resolution Cryo-EM structure of the Type VI secretion membrane complex
<i>In situ</i> and high-resolution Cryo-EM structure of the Type VI secretion membrane complex Open
Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is related to Myoviridae phages. The T6SS i…