Results 31 to 40 of about 180,875 (351)
EasyModel: a user-friendly web-based interface based on MODELLER
Scientific Reports, 2023 Three-dimensional protein structures are invaluable sources of information for the functional annotation of protein molecules. Describing the function of a protein sequence is one of the most common problems in biology.
Seyed Shahriar Arab, Alireza Dantism
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Self-Supervised Pre-training for Protein Embeddings Using Tertiary Structures
AAAI Conference on Artificial Intelligence, 2022 The protein tertiary structure largely determines its interaction with other molecules. Despite its importance in various structure-related tasks, fully-supervised data are often time-consuming and costly to obtain.
Yuzhi Guo +3 more
semanticscholar +1 more source
Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques
Molecules, 2020 We discuss the use of the regularized linear discriminant analysis (LDA) as a model reduction technique combined with particle swarm optimization (PSO) in protein tertiary structure prediction, followed by structure refinement based on singular value ...
Óscar Álvarez-Machancoses +2 more
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Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function
Peptide Science, 2020 Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions.
H. Merritt, N. Sawyer, P. Arora
semanticscholar +1 more source
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
Nucleic Acids Res., 2014 Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models ...
M. Biasini +10 more
semanticscholar +1 more source
Ultrasonics Sonochemistry, 2023 The effects of air thawing (AT), water immersion thawing (WT), microwave thawing (MT) and ultrasound combined with slightly acidic electrolyzed water thawing (UST) on the myofibrillar protein (MP) properties (surface hydrophobicity, solubility, turbidity,
Dewei Kong +8 more
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A Review of Deep Generative Models for Distance Matrices in Protein Structure Modeling [PDF]
IJCI International Journal of Computers and InformationDeep generative models are being explored as a promising approach for generating distance matrix representations of protein tertiary structures. These models capture the complex spatial arrangement of amino acid residues, but challenges remain in ...
Aalaa Sehsah, Afaf Mousa, Gamal Elhady
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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 +2 more
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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 +7 more
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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
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