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Specific Features of the Bank Vole Clethrionomys glareolus Marker Genes’ Expression Representing the Ecotoxicological Effects of a Dioxin-Contaminated Environment
AbstractIt is impossible to reliably evaluate the ecotoxicity of small subtoxic doses of dioxins without duly taking into account how the factors of...
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FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe
Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose...
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Protein binding sites for drug design
Drug development is a lengthy and challenging process that can be accelerated at early stages by new mathematical approaches and modern computers....
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Computational Methods for Protein Tertiary Structure Analysis
Protein folding accuracy is fundamental to all cells. In spite of this, it is difficult to maintain the fidelity of protein synthesis and folding due...
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AI-Assisted Methods for Protein Structure Prediction and Analysis
Proteins are the workhorses of cells. Their sequence is determined by the genetic code embedded in the DNA, which translates it faithfully into a...
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Protein language models can capture protein quaternary state
BackgroundDetermining a protein’s quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein...
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Residue-wise local quality estimation for protein models from cryo-EM maps
An increasing number of protein structures are being determined by cryogenic electron microscopy (cryo-EM). Although the resolution of determined...
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Membrane Protein Production in Escherichia coli: Protocols and Rules
Despite recent progresses in the use of eukaryotic expression system, production of membrane proteins for structural studies still relies on...
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Modeling Protein Complexes and Molecular Assemblies Using Computational Methods
Many biological molecules are assembled into supramolecular complexes that are necessary to perform functions in the cell. Better understanding and...
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From Genome Mining to Protein Engineering: A Structural Bioinformatics Route
This chapter outlines applications in genome mining, along with computational methods to predict protein structure and protein-ligand docking. It...
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Protein Structural Analysis by Cryogenic Electron Microscopy
Cryogenic electron microscopy (cryo-EM) is constantly develo** and growing as a major technique for structure determination of protein complexes....
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Affinity-Purification Combined with Crosslinking Mass Spectrometry for Identification and Structural Modeling of Host–Pathogen Protein–Protein Complexes
Host–pathogen protein–protein interactions are highly complex and dynamic and mediate key steps in pathogen adhesion to host, host invasion, and...
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Opportunities and challenges in design and optimization of protein function
The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design...
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Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy
BackgroundProtein–protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into...
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Monte Carlo Approaches to Study Protein Conformation Ensembles
The molecular dynamics (MD) simulation method is widely used to determine the protein folding sampling by applying various force fields. The results...
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Spatial Models of Piezo Proteins and Protein‒Protein Interaction Networks in Trichoplax Animals (Placozoa)
AbstractThe marine free-living organism Trichoplax (phylum Placozoa) resembles a unicellular amoeba in shape and type of movement. Trichoplax ...
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Image-centric compression of protein structures improves space savings
BackgroundBecause of the rapid generation of data, the study of compression algorithms to reduce storage and transmission costs is important to...
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Direct prediction of intrinsically disordered protein conformational properties from sequence
Intrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are...
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Peptide-Protein Interface Classification Using Convolutional Neural Networks
Peptides are short chains of amino acid residues linked through peptide bonds, whose potential to act as protein inhibitors has contributed to the...
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Using NMR Titration Experiments to Study E. coli FAS-II- and AcpP-Mediated Protein–Protein Interactions
Acyl carrier proteins (ACPs) are central to many primary and secondary metabolic pathways. In E. coli fatty acid biosynthesis (FAB), the central ACP,...