Results 11 to 20 of about 319,877 (305)

Generative Adversarial Learning of Protein Tertiary Structures [PDF]

Molecules, 2021
Protein molecules are inherently dynamic and modulate their interactions with different molecular partners by accessing different tertiary structures under physiological conditions. Elucidating such structures remains challenging.
Taseef Rahman, Yuanqi Du, Liang Zhao, Amarda Shehu   +3 more
doaj   +3 more sources

Recent Progress of Protein Tertiary Structure Prediction

Molecules
The prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades.
Qiqige Wuyun, Yihan Chen, Yifeng Shen, Yang Cao, Gang Hu, Wei Cui, Jianzhao Gao, Wei Zheng   +7 more
doaj   +3 more sources

Protein Macrocyclization for Tertiary Structure Stabilization [PDF]

ChemBioChem, 2021
AbstractProteins possess unique molecular recognition capabilities and enzymatic activities, features that are usually tied to a particular tertiary structure. To make use of proteins for biotechnological and biomedical purposes, it is often required to enforce their tertiary structure in order to ensure sufficient stability under the conditions ...
Anissa Haim, Saskia Neubacher, Tom N. Grossmann   +2 more
openaire   +3 more sources

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

Protein secondary structure: Entropy, correlations and prediction [PDF]

, 2003
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions?
Brenner, Steven E., Crooks, Gavin E.
core   +6 more sources

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

A Hierarchical Approach to Protein Molecular Evolution [PDF]

, 1999
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with Monte Carlo ...
Crameri, Cwirla, Davidson, Devlin, Fisch, Gilbert, Gilbert, Gram, Griffiths, Hawkins, Kamtekar, Kauffman, Kauffman, Kepler, L. D. Bogarad, Lawrence, M. W. Deem, Maeshiro, Mandecki, Moore, Netzer, Patten, Pennisi, Perelson, Riddle, Scott, Shapiro, Shapiro, Stemmer, Stemmer, Zhang   +30 more
core   +2 more sources

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