[HTML][HTML] Can predicted protein 3D structures provide reliable insights into whether missense variants are disease associated?

S Ittisoponpisan, SA Islam, T Khanna, E Alhuzimi… - Journal of molecular …, 2019 - Elsevier
Abstract Knowledge of protein structure can be used to predict the phenotypic consequence
of a missense variant. Since structural coverage of the human proteome can be roughly …

Wide spectrum of NR5A1‐related phenotypes in 46, XY and 46, XX individuals

S Domenice, AZ Machado, FM Ferreira… - … Research Part C …, 2016 - Wiley Online Library
Steroidogenic factor 1 (NR5A1, SF‐1, Ad4BP) is a transcriptional regulator of genes
involved in adrenal and gonadal development and function. Mutations in NR5A1 have been …

New binding sites, new opportunities for GPCR drug discovery

HCS Chan, Y Li, T Dahoun, H Vogel, S Yuan - Trends in biochemical …, 2019 - cell.com
Many central biological events rely on protein–ligand interactions. The identification and
characterization of protein-binding sites for ligands are crucial for the understanding of …

Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport

J Stourac, O Vavra, P Kokkonen, J Filipovic… - Nucleic acids …, 2019 - academic.oup.com
Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels,
and study of the ligands' transport through these transport pathways. Caver Web is the first …

CageCavityCalc (C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages

V Martí-Centelles, TK Piskorz… - Journal of Chemical …, 2024 - ACS Publications
Organic (porous) and metal–organic cages are promising biomimetic platforms with diverse
applications spanning recognition, sensing, and catalysis. The key to the emergence of …

The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters

T Wagner, U Ermler, S Shima - Science, 2016 - science.org
Biological methane formation starts with a challenging adenosine triphosphate (ATP)–
independent carbon dioxide (CO2) fixation process. We explored this enzymatic process by …

Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity

SM Kim, SH Kang, J Lee, Y Heo, EG Poloniataki… - Nature …, 2024 - nature.com
Fe‒S cluster-harboring enzymes, such as carbon monoxide dehydrogenases (CODH),
employ sophisticated artificial electron mediators like viologens to serve as potent …

D3Pockets: a method and web server for systematic analysis of protein pocket dynamics

Z Chen, X Zhang, C Peng, J Wang, Z Xu… - Journal of chemical …, 2019 - ACS Publications
The intrinsic dynamic properties of the ligand-binding pockets of proteins are important for
the protein function mechanism and thus are useful to drug discovery and development. Few …

An atomic model for the human septin hexamer by cryo-EM

DC Mendonça, SL Guimarães, HDM Pereira… - Journal of molecular …, 2021 - Elsevier
In order to form functional filaments, human septins must assemble into hetero-oligomeric
rod-like particles which polymerize end-to-end. The rules governing the assembly of these …

[HTML][HTML] Open source molecular modeling

S Pirhadi, J Sunseri, DR Koes - Journal of Molecular Graphics and …, 2016 - Elsevier
The success of molecular modeling and computational chemistry efforts are, by definition,
dependent on quality software applications. Open source software development provides …