Publications associées à Protein Data Bank

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

De novo design of protein interactions with learned surface fingerprints

Didier Trono, Henning Paul-Julius Stahlberg, Beat Fierz, Priscilla Turelli, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Sandrine Madeleine Suzanne Georgeon, Dongchun Ni, Andreas Scheck, Michael Bronstein

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

2023

Vanadium complexes with N-heterocyclic vinylidene ligands

Rosario Scopelliti, Kay Severin, Farzaneh Fadaei Tirani, Laura Piveteau, Bastiaan Kooij, Zhaowen Dong, Paul Varava

The preparation and the structural characterization of vanadium complexes with terminal and bridging N-heterocyclic vinylidene ligands is reported. The synthesis of the complexes was enabled by utilization of diazoolefins as ligand precursors. Structural d ...

Royal Society of Chemistry2022

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

Stefano Zamuner

Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference ...

PUBLIC LIBRARY SCIENCE2022

Amplitude and phase reconstruction for Low-Energy Electron Holography of individual proteins

Hannah Julia Ochner

Single-molecule imaging methods are of importance in structural biology, and specifically in the imaging of proteins, since they can elucidate conformational variability and structural changes that might be lost in imaging methods relying on averaging proc ...

EPFL2022

cell2mol: encoding chemistry to interpret crystallographic data

Rubén Laplaza Solanas, Anne-Clémence Corminboeuf, Sergio Vela Llausi, Yuri Cho

The creation and maintenance of crystallographic data repositories is one of the greatest data-related achievements in chemistry. Platforms such as the Cambridge Structural Database host what is likely the most diverse collection of synthesizable molecules ...

NATURE PORTFOLIO2022

A long-term study on structural changes in calcium aluminate silicate hydrates

Christian Ludwig, Barbara Lothenbach, Sonya Barzgar, Yu Yan, Mohamed Tarik

Production of blended cements in which Portland cement is combined with supplementary cementitious materials (SCM) is an effective strategy for reducing the CO2 emissions during cement manufacturing and achieving sustainable concrete production. However, t ...

SPRINGER2022

Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors

Sarah Wehrle

Proteins are the basic building blocks necessary for the operation and regulation of virtually all functions in living organisms. Over millions of years, evolution has created a vast repertoire of proteins finely tuned to execute their biological functions ...

EPFL2022

Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples

Loïc Dayon

Background: Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinica ...

ELSEVIER SCI LTD2022

Azole-Based Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors

Pierre Vogel, Florence Pojer, Somi Reddy Majjigapu, George Coukos, Olivier Michielin

The heme enzyme indoleamine 2,3-dioxygenase 1 (IDO1) plays an essential role in immunity, neuronal function, and aging through catalysis of the rate-limiting step in the kynurenine pathway of tryptophan metabolism. Many IDO1 inhibitors with different chemo ...

AMER CHEMICAL SOC2021