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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Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction [PDF]
, 2008 Background: We present a novel method of protein fold decoy discrimination using machine learning, more specifically using neural networks. Here, decoy discrimination is represented as a machine learning problem, where neural networks are used to learn ...
Jones, DT +3 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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Comparative analysis of low-frequency vibrational spectra of native and denatured proteins [PDF]
Известия Саратовского университета. Новая серия: ФизикаBackground 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. +2 more
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Refinement of Protein Tertiary Structure by Using Spin-Spin Coupling Constants from Nuclear Magnetic Resonance Measurements [PDF]
, 2012 Modelling protein structure seems a challenging enterprise because the number of structure parameters required ordinarily exceeds the amount of independent data points available from experimental observations. Expressing the predominant conformation of a
Schmidt, Jürgen M. +5 more
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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 +3 more
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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 +7 more
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Oxidation of tertiary amine-derivatized surfaces to control protein adhesion [PDF]
, 2013 Selective oxidation of omega-tertiary amine self-assembled thiol monolayers to tertiary amine N-oxides is shown to transform the adhesion of model proteins lysozyme and fibrinogen upon them.
Evans, Stephen D. +12 more
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