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DeepBSRPred: deep learning-based binding site residue prediction for proteins
MotivationProteins–protein interactions (PPIs) are important to govern several cellular activities. Amino acid residues, which are located at the...
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Crop Residue Management
Managing crop residues is of paramount importance for soil and water conservation (Fu et al. 2021). Crop residues include leaves, stalks, cobs,...
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Analysis of residue–residue interactions in the structures of ASIC1a suggests possible gating mechanisms
The gating mechanism of acid-sensitive ion channels (ASICs) remains unclear, despite the availability of atomic-scale structures in various...
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Biomass Technologies for Crop Residue Management
In India, large-scale agricultural farming practices are continuously performed from man immemorial. During crop harvesting, a huge quantity of its...
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Binding Proteins
This chapter pivots to the microscopic world of skeletal muscle-binding proteins—these molecular powerhouses that perform many tasks essential to the...
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Inter-helical Residue Contact Prediction in \(\alpha \) -Helical Transmembrane Proteins Using Structural Features
Residue contact maps offer a 2-d, reduced representation of 3-d protein structures and constitute a structural constraint and scaffold in structural...
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Spike-and-ACE2 Binding with 100 Drugs
Durdagi (All atom 500-nano seconds molecular dynamics simulations of SARS-CoV-2 spike receptor-binding domain bound with ACE2 (Version 2) [Data set]....
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SOFB is a comprehensive ensemble deep learning approach for elucidating and characterizing protein-nucleic-acid-binding residues
Proteins and nucleic-acids are essential components of living organisms that interact in critical cellular processes. Accurate prediction of nucleic...
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Enzymatic Modification of Potato Residue Fiber Improves Cholesterol and Sugar Absorption
Potato residue is rich in dietary fiber (DF) but low in soluble dietary fiber (SDF), and modification is required to generate high-quality DF. In...
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D3PM: a comprehensive database for protein motions ranging from residue to domain
BackgroundKnowledge of protein motions is significant to understand its functions. While currently available databases for protein motions are mostly...
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Spatial covariance analysis reveals the residue-by-residue thermodynamic contribution of variation to the CFTR fold
Although the impact of genome variation on the thermodynamic properties of function on the protein fold has been studied in vitro, it remains a...
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Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter
Sucrose import from photosynthetic tissues into the phloem is mediated by transporters from the low-affinity sucrose transporter family (SUC/SUT...
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Role of Lactic Acid Bacteria in Insecticide Residue Degradation
Lactic acid bacteria are gaining global attention, especially due to their role as a probiotic. They are increasingly being used as a flavoring agent...
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MetaLLM: Residue-Wise Metal Ion Prediction Using Deep Transformer Model
Proteins bind to metals such as copper, zinc, magnesium, etc., serving various purposes such as importing, exporting, or transporting metal in other...
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Repurposing of drugs targeting heparan sulphate binding site of dengue virus envelope protein: an in silico competitive binding study
Dengue virus, an arbovirus, leads to millions of infections every year ultimately leading to a high rate of mortality. Highly effective and specific...
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Repurposing of therapeutic antibodies against dengue virus envelope protein receptor binding domain
Dengue virus (DENV) is the leading cause of numerous deaths every year due to its high infectivity. In this study we have tried to target the DENV...
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Barley AGO4 proteins show overlap** functionality with distinct small RNA-binding properties in heterologous complementation
Key messageBarley AGO4 proteins complement expressional changes of epigenetically regulated genes in Arabidopsis ago4-3 mutant and show a distinct...
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Computational study on the binding mechanism of allosteric drug TNO155 inhibiting SHP2E76A
E76A mutations of SHP2 have been reported to associate with genetic developmental diseases and cancers, and TNO155 is one of the effective inhibitors...
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Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope map**
Precise epitope determination of therapeutic antibodies is of great value as it allows for further comprehension of mechanism of action, therapeutic...
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Spike RBDs Binding with 50 Drugs
Shaw et al. (2020) selected 5152 drug molecules from the FDA drug library and found that during 2...