Results 81 to 90 of about 106,304 (285)

Analysing the significance of small conformational changes and low occupancy states in serial crystallographic data

FEBS Open Bio, EarlyView.
This protocol paper outlines methods to establish the success of a time‐resolved serial crystallographic experiment, by means of statistical analysis of timepoint data in reciprocal space and models in real space. We show how to amplify the signal from excited states to visualise structural changes in successful experiments.
Jake Hill, Yelyzaveta Pulnova, Elke De Zitter, Helen M. Ginn, Briony A. Yorke   +4 more
wiley   +1 more source

Crystal structure prediction based on diffusion model and graph network optimization

JPhys Materials
Accurately and quickly predicting the crystal structures of unknown materials can significantly accelerate the discovery of new materials. However, stable crystal structures only exist at the global minimum of formation energy, making optimization based ...
Tao Hong, Jiong Yang, Guixin Cao
doaj   +1 more source

Evolutionarily divergent DUF4465 domains have a common vitamin B12‐binding function

FEBS Open Bio, EarlyView.
We show that DUF4465 family proteins, widespread across bacteria from gut microbiomes, hydrothermal vents, and soil, share a common vitamin B12‐binding function. These augmented β‐jellyroll proteins bind vitamin B12 via extended loops. Our findings establish sequence‐diverse DUF4465 proteins as a widespread class of B12‐binding proteins, highlighting ...
Charlea Clarke, Michal Banasik, Rokas Juodeikis, Martin J. Warren, Richard W. Pickersgill   +4 more
wiley   +1 more source

Blind testing cross-linking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11) [version 1; referees: 1 approved, 2 approved with reservations]

Wellcome Open Research, 2016
Determining the structure of a protein by any method requires various contributions from experimental and computational sides. In a recent study, high-density cross-linking/mass spectrometry (HD-CLMS) data in combination with ab initio structure ...
Adam Belsom, Michael Schneider, Lutz Fischer, Mahmoud Mabrouk, Kolja Stahl, Oliver Brock, Juri Rappsilber   +6 more
doaj   +1 more source

Molecular dynamics simulations of positively selected codons in FcγRI reveal novel biochemical binding properties

FEBS Open Bio, EarlyView.
Evolutionary analysis across 32 placental mammals identified positive selection at residues H148 and W149 in the immune receptor FcγR1. Ancestral reconstruction combined with molecular dynamics simulations reveals how these mutations may influence receptor structure and dynamics, providing insight into the evolution of antibody recognition and immune ...
David A. Young, Omar Arias‐Gaguancela, Fiona Gibson, Morgan Grainger, Jodie Score, Amit Nathubhai, Mauricio Cafiero, Lee Richard Machado   +7 more
wiley   +1 more source

UiO‐66 metal–organic frameworks in biomedicine: From structural tunability to bioimaging, photodiagnostics, and photodynamic cancer therapy

FEBS Open Bio, EarlyView.
UiO‐66(Zr) metal–organic frameworks are chemically stable, biocompatible, and highly tunable nanomaterials. Their modular structure enables controlled drug delivery, multimodal bioimaging, and light‐activated photodynamic therapy, supporting integrated diagnostic and therapeutic (theranostic) applications in cancer and biomedical research.
Veronika Huntošová, Grigorii Rakhalskii, Miroslav Almáši   +2 more
wiley   +1 more source

AlphaCrystal: Contact map based crystal structure prediction using deep learning

, 2023
Crystal structure prediction is one of the major unsolved problems in materials science. Traditionally, this problem is formulated as a global optimization problem for which global search algorithms are combined with first principle free energy ...
Yang, Wenhui, Siriwardane, Edirisuriya MD, Hu, Jianjun, Li, Qin, Zhao, Yong, Dong, Rongzhi, Song, Yuqi   +6 more
core  

Structure prediction of porous organic crystals

RSC Advances
In this work, we explore the possibility of applying automated crystal structure prediction to reproduce the experimentally identified metastable porous polymorphs.
Musiha Mahfuza Mukta, Romain Perriot, Shinnosuke Hattori, Wei Zhou, Qiang Zhu   +4 more
openaire   +2 more sources

Equivariant Diffusion for Crystal Structure Prediction

CoRR
In addressing the challenge of Crystal Structure Prediction (CSP), symmetry-aware deep learning models, particularly diffusion models, have been extensively studied, which treat CSP as a conditional generation task. However, ensuring permutation, rotation, and periodic translation equivariance during diffusion process remains incompletely addressed. In
Peijia Lin, Pin Chen, Rui Jiao, Qing Mo, Jianhuan Cen, Wenbing Huang 0001, Yang Liu 0005, Dan Huang 0001, Yutong Lu   +8 more
openaire   +3 more sources

Graph-text contrastive learning of inorganic crystal structure toward a foundation model of inorganic materials

Science and Technology of Advanced Materials: Methods
Developing foundation models for materials science has attracted attention. However, there is a lack of studies on inorganic materials due to the difficulty in the comprehensive representation of geometric concepts composing crystals: local atomic ...
Keisuke Ozawa, Teppei Suzuki, Shunsuke Tonogai, Tomoya Itakura   +3 more
doaj   +1 more source