From integrative structural biology to cell biology

A Sali - Journal of Biological Chemistry, 2021 - jbc.org
Integrative modeling is an increasingly important tool in structural biology, providing
structures by combining data from varied experimental methods and prior information. As a …

[HTML][HTML] Hybrid methods for combined experimental and computational determination of protein structure

JT Seffernick, S Lindert - The Journal of chemical physics, 2020 - pubs.aip.org
Knowledge of protein structure is paramount to the understanding of biological function,
develo** new therapeutics, and making detailed mechanistic hypotheses. Therefore …

CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps

M Shekhar, G Terashi, C Gupta, D Sarkar… - Matter, 2021 - cell.com
Cryoelectron microscopy requires molecular modeling for refinement of structures.
Ensemble models arrive at low free-energy molecular structures, but are computationally …

[HTML][HTML] Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB

W Chiu, MF Schmid, GD Pintilie, CL Lawson - Journal of Biological …, 2021 - Elsevier
Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to
study thin and periodic arrays of proteins. Following a half-century of development in cryo …

Improving SARS-CoV-2 structures: Peer review by early coordinate release

TI Croll, CJ Williams, VB Chen, DC Richardson… - Biophysical journal, 2021 - cell.com
This work builds upon the record-breaking speed and generous immediate release of new
experimental three-dimensional structures of the severe acute respiratory syndrome …

CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics

M Shekhar, G Terashi, C Gupta, G Debussche… - bioRxiv, 2019 - biorxiv.org
Cryo-EM is a powerful method for determining biomolecular structures. But, unlike X-ray
crystallography or solution-state NMR, which are data-rich, cryo-EM can be data-poor. Cryo …

League of Brazilian Bioinformatics: a competition framework to promote scientific training

LM Carvalho, NAR Coimbra, MRC Neves, NJ Fonseca… - bioRxiv, 2020 - biorxiv.org
Background the scientific training to become a bioinformatician includes multidisciplinary
abilities, which increase the challenges to professional development. Competition …

Synthqa-hierarchical machine learning-based protein quality assessment

M Korovnik, K Hippe, J Hou, D Si, K Kishaba, R Cao - bioRxiv, 2021 - biorxiv.org
Motivation It has been a challenge for biologists to determine 3D shapes of proteins from a
linear chain of amino acids and understand how proteins carry out life's tasks. Experimental …