Results 21 to 30 of about 168,206 (155)

Evaluating Autoencoder-Based Featurization and Supervised Learning for Protein Decoy Selection

Molecules, 2020
Rapid growth in molecular structure data is renewing interest in featurizing structure. Featurizations that retain information on biological activity are particularly sought for protein molecules, where decades of research have shown that indeed ...
Fardina Fathmiul Alam, Taseef Rahman, Amarda Shehu   +2 more
doaj   +1 more source

CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins

BMC Bioinformatics, 2023
Background CRISPR-Cas-Docker is a web server for in silico docking experiments with CRISPR RNAs (crRNAs) and Cas proteins. This web server aims at providing experimentalists with the optimal crRNA-Cas pair predicted computationally when prokaryotic ...
Ho-min Park, Jongbum Won, Yunseol Park, Esla Timothy Anzaku, Joris Vankerschaver, Arnout Van Messem, Wesley De Neve, Hyunjin Shim   +7 more
doaj   +1 more source

De novo protein structure prediction using ultra-fast molecular dynamics simulation. [PDF]

PLoS ONE, 2018
Modern genomics sequencing techniques have provided a massive amount of protein sequences, but experimental endeavor in determining protein structures is largely lagging far behind the vast and unexplored sequences.
Ngaam J Cheung, Wookyung Yu
doaj   +1 more source

CASP11--An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline. [PDF]

PLoS ONE, 2016
In silico prediction of a protein's tertiary structure remains an unsolved problem. The community-wide Critical Assessment of Protein Structure Prediction (CASP) experiment provides a double-blind study to evaluate improvements in protein structure ...
Axel W Fischer, Sten Heinze, Daniel K Putnam, Bian Li, James C Pino, Yan Xia, Carlos F Lopez, Jens Meiler   +7 more
doaj   +1 more source

Comparative analysis of low-frequency vibrational spectra of native and denatured proteins [PDF]

Известия Саратовского университета. Новая серия: Физика
Background and Objectives: Changes in the secondary and tertiary structures of protein molecules during thermal denaturation lead to changes in their vibrational spectra.
Mankova, Anna A., Brandt, Nikolay Nikolaevich, Chikishev, Andrey Yu.   +2 more
doaj   +1 more source

Interaction Of Calcium Phosphate Nanoparticles With Human Chorionic Gonadotropin Modifies Secondary And Tertiary Protein Structure

Nova Biotechnologica et Chimica, 2015
Calcium phosphate nanoparticles (CaPNP) have good biocompatibility and bioactivity inside human body. In this study, the interaction between CaPNP and human chorionic gonadotropin (hCG) was analyzed to determine the changes in the protein structure in ...
Al-Hakeim Hussein K, Al-Zabeba Rahman S., Grulke Eric, Jaffar Al-Mulla Emad A.   +3 more
doaj   +1 more source

Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network

Biomolecules, 2022
Heme proteins serve diverse and pivotal biological functions. Therefore, clarifying the mechanisms of these diverse functions of heme is a crucial scientific topic. Distortion of heme porphyrin is one of the key factors regulating the chemical properties
Hiroko X. Kondo, Hiroyuki Iizuka, Gen Masumoto, Yuichi Kabaya, Yusuke Kanematsu, Yu Takano   +5 more
doaj   +1 more source

An Algebro-topological description of protein domain structure. [PDF]

PLoS ONE, 2011
The space of possible protein structures appears vast and continuous, and the relationship between primary, secondary and tertiary structure levels is complex.
Robert Clark Penner, Michael Knudsen, Carsten Wiuf, Jørgen Ellegaard Andersen   +3 more
doaj   +1 more source

Bioinformatics Analysis of the NOT5 Gene in Saccharomyces uvarum

Shipin gongye ke-ji, 2022
Objective: In this paper, we obtained the NOT5 gene from Saccharomyces uvarum by transcriptome analysis. Analysis of its biological information can lay the foundation for the later study of the role of the gene.
Shujin DING, Yanping YANG, Ruyou DENG, Fuxian MA, Tuo YIN, Hanyao ZHANG   +5 more
doaj   +1 more source

Human growth hormone inclusion bodies present native-like secondary and tertiary structures which can be preserved by mild solubilization for refolding

Microbial Cell Factories, 2022
Background Native-like secondary structures and biological activity have been described for proteins in inclusion bodies (IBs). Tertiary structure analysis, however, is hampered due to the necessity of mild solubilization conditions.
Rosa Maria Chura-Chambi, Chuck Shaker Farah, Ligia Morganti   +2 more
doaj   +1 more source