Results 101 to 110 of about 326,099 (315)

SuperLigands – a database of ligand structures derived from the Protein Data Bank

BMC Bioinformatics, 2005
Background Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds.
Preissner Robert, Goede Andrean, Dunkel Mathias, Michalsky Elke   +3 more
doaj   +1 more source

pdb-eda

, 2019
Code, intermediate data, and results for:Yao, Sen, et al. "A chemical interpretation of protein electron density maps in the worldwide Protein Data Bank." Plos one, Computational ...
Hunter Moseley (3343412), Sen Yao (3343238)   +1 more
core   +1 more source

Exon 7 splicing of ERα predicts poor prognosis and increases phenotypic heterogeneity in luminal a subtype breast cancer

FEBS Open Bio, EarlyView.
ERα splice variant ERα∆7 lacks the C‐terminus, and its expression may change phenotypes of breast cancers. Our results showed that ERα∆7 is found in the luminal A subtype, and elevated ERα∆7 levels are linked to improved cell survival with lower proliferation and migration.
Long Wai Tsui, Taobo Hu, Thomson Christian Husein, Wai Hei Shek, Bingrong Chen, Depeng Wang, Shu Wang, Weichuan Yu, Xiaodan Fan, Mengping Long, Toyotaka Ishibashi   +10 more
wiley   +1 more source

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

PDB-Metrics: a web tool for exploring the PDB contents.

Genetics and molecular research : GMR, 2006
PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein sequence, structure and function. It summarizes the characteristics of the collection of protein structure descriptions deposited in the Protein Data Bank (PDB) and provides a Web interface to ...
Renato, Fileto, Paula R, Kuser, Michel E B, Yamagishi, André A, Ribeiro, Thiago G, Quinalia, Eduardo H, Franco, Adauto L, Mancini, Roberto H, Higa, Stanley R M, Oliveira, Edgard H, Santos, Fabio D, Vieira, Ivan, Mazoni, Sergio A B, Cruz, Goran, Neshich   +13 more
openaire   +1 more source

PCDDB: the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata

, 2010
The Protein Circular Dichroism Data Bank (PCDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their associated experimental metadata.
Klose, D.P., Benjamin Woollett, B. A. Wallace, Woollett, Benjamin, Janes, R.W., Wallace, Bonnie A., Robert W. Janes, Lee Whitmore, Andrew John Miles, Whitmore, Lee, Miles, Andrew J., D. P. Klose   +11 more
core   +1 more source

YlmG1 is localized exclusively to the chloroplast envelope membrane and is involved in preprotein translocation in Arabidopsis thaliana

FEBS Open Bio, EarlyView.
Cytosolically synthesized chloroplast preproteins are translocated across the outer and inner envelope membranes through translocons called TOC and TIC, respectively. In green algae and plants, the TIC core is composed of essential membrane proteins, Tic12, Tic20, and Tic214.
Mengyi Li, Xueyang Zhao, Masato Nakai
wiley   +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

PDB-Metrics: a web tool for exploring the PDB contents. [PDF]

, 2017
. PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein sequence, structure and function. It summarizes the characteristics of the collection of protein
YAMAGISHI, M. E. B., FILETO, R., FRANCO, E. H., RIBEIRO, A. A., MANCINI, A. L., HIGA, R. H., OLIVEIRA, S. R. M., KUSER, P. R., QUINALIA, T. G., NESHICH, G., CRUZ, S. A. B., SANTOS, E. H., MAZONI, I., VIEIRA, F. D.   +13 more
core  

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