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Protein Data Bank
Related publications (60)
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 ...
EPFL2023De 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, Michael Bronstein, Pablo Gainza Cirauqui, Zander Harteveld, Andreas Scheck, Charlène Mireille Raymonde Raclot, Anthony Marchand, Alexandra Teslenko, Casper Alexander Goverde, Aaron Simone Petruzzella, Stephen Michael Buckley, Martin Pacesa, Stéphane Rosset, Sarah Wehrle, Freyr Sverrisson, Alexandra Krina Van Hall-Beauvais, Jane Marsden
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 ...
2023Vanadium 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 ...
2022Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules
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 SCIENCE2022Amplitude and phase reconstruction for Low-Energy Electron Holography of individual proteins
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 ...
EPFL2022cell2mol: encoding chemistry to interpret crystallographic data
Rubén Laplaza Solanas, Yuri Cho, Sergio Vela Llausi
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 PORTFOLIO2022A 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 ...
SPRINGER2022Azole-Based Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors
Pierre Vogel, Florence Pojer, George Coukos, Somi Reddy Majjigapu, 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 SOC2021Three-membered cyclic digermylenes stabilised by an N-heterocyclic carbene dagger
Treatment of potassium salts of silole dianions with donor stabilised germanium dichlorides gave the anticipated silagermafulvenylidenes R2Si = Ge(Do) (R2Si = 1-silacyclopentadiendiyl, Do = N-heterocyclic carbene (NHC)) only as transient intermediates in a ...
ROYAL SOC CHEMISTRY20213D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme
Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases composed of 180kDa subunits (L-GDHs(180)) contain long N- and C-terminal segments flanking the catalytic core. Desp ...
2021