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The functional motions and related key residues behind the uncoating of coxsackievirus A16

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2021; 89 (10)

The coxsackievirus A16 (CVA16) is a highly contagious virus that causes the hand, foot, and mouth disease, which seriously threatens the health of chi......

Mycobacterium tuberculosis puromycin hydrolase displays a prolyl oligopeptidase fold and an acyl aminopeptidase activity

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, ; ()

Puromycin-hydrolizing peptidases have been described as members of the prolyl oligopeptidase peptidase family. These enzymes are present across all do......

Exploration of key residues and conformational change of anti-terminator protein GlpP for ligand and RNA binding

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, ; ()

Anti-terminator protein GlpP regulates gene expression of glycerol uptake operon at post-transcriptional level in a number of bacteria. By now, the mo......

Structural insights into the thermostability mechanism of a nitrile hydratase from Caldalkalibacillus thermarum by comparative molecular dynamics simulation

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, ; ()

Nitrile hydratase (NHase), an excellent bio-catalyst for the synthesis of amide compounds, was composed of two heterologous subunits. A thermoalkaliph......

Study on functional sites in human multidrug resistance protein 1 (hMRP1)

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, ; ()

Human multidrug resistance protein 1 (hMRP1) is an important member of the ATP-binding cassette (ABC) transporter superfamily. It can extrude a variet......

Crystallographic and modeling study of the human inorganic pyrophosphatase 1: A potential anti-cancer drug target

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, ; ()

Inorganic pyrophosphatases (PPases) catalyze the hydrolysis of pyrophosphate to phosphates. PPases play essential roles in growth and development, and......

Investigating the folding mechanism of the N-terminal domain of ribosomal protein L9

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, ; ()

Protein folding is a popular topic in the life science. However, due to the limited sampling ability of experiments and simulations, the general foldi......

Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, ; ()

Molecular dynamics (MD) simulations are a popular method of studying protein structure and function, but are unable to reliably sample all relevant co......

Insights into specificity and catalytic mechanism of amphotericin B/nystatin thioesterase

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2021; 89 (5)

Polyene polyketides amphotericin B (AMB) and nystatin (NYS) are important antifungal drugs. Thioesterases (TEs), located at the last module of PKS, co......

Crystal structure of a novel fold protein Gp72 from the freshwater cyanophage Mic1

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2020; 88 (9)

Cyanophages, widespread in aquatic systems, are a class of viruses that specifically infect cyanobacteria. Though they play important roles in modulat......

Performance of human and server prediction inCAPRIrounds 38-45

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2020; 88 (8)

CAPRI challenges offer a variety of blind tests for protein-protein interaction prediction. In CAPRI Rounds 38-45, we generated a set of putative bind......

C1188Dmutation abolishes specific recognition betweenMLL1-CXXCdomain andCpGsite by inducing conformational switch of flexible N-terminal

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2020; 88 (11)

Mixed lineage leukemia protein (MLL1 protein) recognizes the CpG site via its CXXC domain and is frequently associated with leukemia. The specific rec......

The characterization of pc-polylines representing protein backbones

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2020; 88 (2)

The backbone of a protein is typically represented as either a C-alpha-polyline, a three-dimensional (3D) polyline that passes through the C-alpha ato......

Challenges and opportunities of automated protein-protein docking: HDOCK server vs human predictions in CAPRI Rounds 38-46

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2020; 88 (8)

Protein-protein docking plays an important role in the computational prediction of the complex structure between two proteins. For years, a variety of......

Template-based modeling and ab-initio docking using CoDock in CAPRI

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2020; 88 (8)

Integration of template-based modeling, global sampling and precise scoring is crucial for the development of molecular docking programs with improved......

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