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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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Mechatronic Ski Binding
Electromechanical components have already arrived in the field of sports equipment, such as changing the suspension fork stiffness of a mountain bike...
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Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing
RNA-binding proteins (RBPs) regulate diverse cellular processes by dynamically interacting with RNA targets. However, effective methods to capture...
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Lipid Binding of SH2 Domains
The Src homology 2 (SH2) domain is a modular protein interaction domain that specifically recognizes the phosphotyrosine (pY) motif of a target...
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Assay of CB1 Receptor Binding
Type-1 cannabinoid receptor (CB1), one of the main targets of endocannabinoids, plays a key role in several pathophysiological conditions that affect...
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Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs
BackgroundAllele-specific binding (ASB) events occur when transcription factors (TFs) bind more favorably to one of the two parental alleles at...
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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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Sequence-Based Nanobody-Antigen Binding Prediction
Nanobodies (Nb) are monomeric heavy-chain fragments derived from heavy-chain only antibodies naturally found in Camelids and Sharks. Their...
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3CLpro Binding with N3/Lopinavir/Ritonavir
This brief chapter is to do molecular dynamics (MD) studies on SARS-CoV-2 3CLpro binding with three inhibitors N3, lopinavir, and ritonavir,...
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Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL
The intrinsically disordered region (IDR) of Bim binds to the flexible cryptic site of Bcl-xL, a pro-survival protein involved in cancer progression...
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Melatonin Inhibits AGS Cell Proliferation by Binding to the ATP Binding Site of CDK2 Under Hyperglycemic Conditions
Cancer cells utilize glucose as their primary energy source. The aggressive nature of cancer cells is therefore enhanced in hyperglycemic conditions....
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Fast Protocols for Characterizing Antibody–Peptide Binding
Microarray assay formats gained popularity in the 1990s, first implemented in DNA-based arrays but later adopted for use with proteins, namely...
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PLpro Binding with 12 Compounds
The papain-like protease (PLpro), a component of the large, multi-domain protein NSP3, is a cysteine protease essential for the replication of...
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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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Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP
Ultraviolet crosslinking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs)....
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Database for Plant Transcription Factor Binding Sites
Reconstruction of gene regulatory networks is a very important but difficult issue in plant sciences. Recently, numerous high-throughput techniques,...
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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...
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Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans
BackgroundTranscription factors (TFs) exhibit heterogeneous DNA-binding specificities in individual cells and whole organisms under natural...
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Assay of GTPγS Binding in Autoradiography
Autoradiography of radiolabeled GTPγS ([35S]GTPγS) binding is a relevant technique to study the function of G protein-coupled receptors (GPCRs) ex...
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Assessing TFAM Binding to Human Mitochondrial DNA
Mitochondrial transcription factor A (TFAM) is a mitochondrial DNA (mtDNA)-binding protein that plays a crucial dual role in the initiation of...