Accurate Prediction of Protein-Binding Residues in Protein Sequences Using SCRIBER.

Deciphering molecular-level mechanisms that govern protein-protein interactions (PPIs) relies in part on the accurate prediction of protein-binding partners and protein-binding residues. These predictions can be used to support a wide spectrum of applications that include development of PPI networks and protein docking programs, drug design studies, and investigations of molecular details that underlie certain diseases. Computational methods that predict protein-binding residues offer convenient, inexpensive, and relatively accurate data that can aid these efforts.

SCAMPER: Accurate Type-Specific Prediction of Calcium-Binding Residues Using Sequence-Derived Features.

Understanding molecular mechanisms involved in calcium-protein interactions and modeling corresponding docking rely on the accurate identification of calcium-binding residues (CaBRs). The defects of experimentally annotating protein functions enhances the development of computational approaches that correctly identify calcium-binding interactions. Studies have reported that current methods severely cross-predict residues that interact with other types of molecules (e.

A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level.

Clear evidence has shown that metal ions strongly connect and delicately tune the dynamic homeostasis in living bodies. They have been proved to be associated with protein structure, stability, regulation, and function. Even small changes in the concentration of metal ions can shift their effects from natural beneficial functions to harmful.

Serum NLRP3 Inflammasome and BDNF: Potential Biomarkers Differentiating Reactive and Endogenous Depression.

Background: The highly heterogeneous pathogenesis of depression and limited response to current antidepressants call for more objective evidence for depression subtypes. Reactive and endogenous depression are two etiologically distinct subtypes associated with different treatment responses. This study aims to explore the potential biomarkers that differentiate reactive and endogenous depressions.

TYLER, a fast method that accurately predicts cyclin-dependent proteins by using computation-based motifs and sequence-derived features.

Cyclins and related cyclin-dependent kinases play vital roles in regulating the progression in the cell cycle. Understanding the intrinsic mechanisms of cyclins promises knowledge about cell uncontrolled proliferation and prevention of cancer cells. Therefore, accurate recognition of cyclins is important for the investigation of tumor cells and biomedical engineering.

[Effect of Acupuncture Intervention on Depression Behavior and Expression of ERK 1/2 and BDNF in Prefrontal Cortex in Chronic Unpredictable Mild Stress Induced Depression Rats].

Objective: To investigate the effect of acupuncture intervention on the depression behavior and expression of extracellular signal-regulated protein kinases (ERK 1/2), p-ERK 1/2 and brain-derived neurotrophic factor (BDNF) in the prefrontal cortex of chronic unpredictable mild stress (CUMS) induced depression rats, so as to explore its antidepressant mechanism.

Methods: Sixty-four male SD rats were randomly divided into control, model, acupuncture, Fluoxetine, model ＋ Dimethyl sulfoxide (DMSO), model ＋ PD 98059(an ERK pathway inhibitor), acupuncture ＋ PD 98059 and Fluoxetine ＋ PD 98059 groups (＝8 rats in each). The CUMS depression model was established by using chronic mild and unpredictable stress methods for 21 days.

Molecular-level effects of acupuncture on depression: a genome-wide transcriptome analysis of pituitary gland in rats exposed to chronic restraint stress.

Objective: To investigate the antidepressant mechanism of acupuncture at the molecular level in the pituitary gland of rats exposed to chronic restraint stress (CRS).

Methods: Forty-eight rats were randomly divided into a control group (C), model group (M), fluoxetine group (F), and acupuncture group (A). CRS was induced in the model group by restraining rats for 28 days.

Mechanisms Underlying the Antidepressant Response of Acupuncture via PKA/CREB Signaling Pathway.

Protein kinase A (PKA)/cAMP response element-binding (CREB) protein signaling pathway, contributing to impaired neurogenesis parallel to depressive-like behaviors, has been identified as the crucial factor involved in the antidepressant response of acupuncture. However, the molecular mechanisms associated with antidepressant response of acupuncture, neurogenesis, and depressive-like behaviors ameliorating remain unexplored. The objective was to identify the mechanisms underlying the antidepressant response of acupuncture through PKA signaling pathway in depression rats by employing the PKA signaling pathway inhibitor H89 in in vivo experiments.