FitDockApp: a Graphical User Interface Plugin for Template-based Docking With PyMOL / 生物化学与生物物理进展

ObjectiveMolecular docking plays a critical role in predicting binding modes and affinity between molecules, serving as a pivotal method in structural biology and computer-aided drug design research. Our research team has recently developed a novel template-based docking method called FitDock, which outperforms commonly used molecular docking methods in terms of accuracy and speed, particularly when approximate protein-ligand templates are available. To enhance the accessibility of the FitDock method and promote its broader application in the field of molecular simulation, the development of a graphical software tool is imperative. MethodsUtilizing Python-based graphical programming, we have created FitDockApp, a plugin software for the molecular visualization software PyMOL. ResultsFitDockApp enables template-based molecular docking and ligand structure alignment through an interactive graphical interface, providing real-time visualization of predicted three-dimensional structures. It also offers the convenience of uploading docking files to a laboratory server to obtain the optimal template. Additionally, FitDockApp includes batch docking functionality. ConclusionFitDockApp simplifies the docking process through its user-friendly interface and provides robust functionality to assist researchers in obtaining precise docking results. FitDockApp is a free software compatible with both Windows and Linux systems and can be downloaded from http://cao.labshare.cn/fitdock/.

A PKLR Gene Novel Complex Mutation in Erythrocyte Pyruvate Kinase Deficiency Detected by Targeted Sequence Capture and Next Generation Sequencing / 中国实验血液学杂志

<p><b>OBJECTIVE</b>To explore the molecular mechanism of erythrocyte pyruvate kinase deficiency (PKD).</p><p><b>METHODS</b>Targeted sequence capture and next-generation sequencing (NGS) were used to detect the regions of exon and exon-intron boundarie of PKLR gene in a clinical suspected PKD patient. The protein function of mutant gene was forecasted by the SIFT and PolyPhen-2 databank, after the mutation of PKLR gene in the patient was detected by the NGS technology, its genotype was confirmed by Sanger sequencing.</p><p><b>RESULTS</b>The patient was found to have peculiar double heterozygous mutations: 661 G>A (Asp221Asn) of exon 5 and 1528 C>T (Arg510Ter) of exon 10, resulting in amino acid substitution Asp221Asn and Arg510Ter, these mutations were also further confirmed by Sanger sequencing. The complex mutations were infrequent and each of them was able to cause diseases.</p><p><b>CONCLUSION</b>The complex mutations of both 661 G>A and 1528 C>T of PKLR gene are the molecular mechanism of PKD. Simultaneous existance of above-mentioned complex mutations in PDK patient was never been previously reported at home and abroad.</p>

Observation on therapeutic effect of Chuzhen therapy on insomnia / 中国针灸

<p><b>OBJECTIVE</b>To evaluate the therapeutic effect of Chuzhen therapy on insomnia through clinical randomized controlled trials.</p><p><b>METHODS</b>Sixty cases of insomnia were randomly divided into a Chuzhen group (n=30) and an acupuncture group (n=30). Acupoints of Bazhen (Baihui Bazhen, Fengfu Bazhen, Shendao Bazhen) and Hechelu [from Dazhui (GV 14) to Mingmen (GV 4)] in the Chuzhen group, and Baihui (GV 20), Sishencong (EX-HN 1), etc. in the acupuncture group were selected, respectively. Four weeks treatments were carried out in the two groups, once daily for 5 times on week days. Three months after treatment, they were followed up and the therapeutic effects were assessed by the effective rate of sleep improvement and Pittsburgh Sleep Quality Index (PSQI).</p><p><b>RESULTS</b>After treatment, the sleep quality in the two groups was improved, but there were no differences in the effective rate of sleep improvement and PSQI between the two groups (all P > 0.05). Three months after treatment, the total effective rate of 85.2% in the Chuzhen group was better than 78.6% in the acupuncture group (P < 0.05). The total cumulative score of PSQI, sleep effectiveness and the factors of sleep obstacle in the Chuzhen group were significantly different from those in the acupuncture group (all P < 0.05).</p><p><b>CONCLUSION</b>Chuzhen therapy can increase long-term sleep quality and living quality through improving the effective rate of sleep and reducing the score of PSQI in the patients of insomnia.</p>

Regulative effects of ERK and P38 signal transduction pathway on cell cycle in chronic myeloid leukemia / 中国实验血液学杂志

This study was aimed to investigate the regulative effect of ERK and p38 signal transduction pathway on cell cycle of CML. The mRNA and protein expression of ERK, p38, cyclin D(2), cyclin E and p27 (ERK and p38 were Phosph-ERK and Phosph-P38) in CML cells and K562 cell lines were detected by RT-PCR and Western blot, respectively; cell cycle was determined by FCM, and their relationship was analyzed. The results showed that the mRNA and protein expressions of ERK, p38, cyclin D(2) and cyclin E in CML cells and K562 cells increased (P<0.01) and the expression of p27 decreased (P<0.01). There was positive correlation between the protein expressions of cyclin D(2) and the protein expression of ERK, p38 and cyclin E, but there was negative correlation between the protein expressions of cyclin D(2) and the protein expression of p27. The percentage of cells in G(0)/G(1) phase was decreased and the percentage of cells in S phase was increased, there was significant difference as compared with control (P<0.05). It is concluded that increase of the mRNA expression and protein activity of ERK and p38 activate the cell cycle-regulating proteins such as cyclin D(2), cyclin E, p27 which results in shortening of G(0)/G(1) phase, switching cell to S phase through G(1)/S check point quickly and accelerating cell cycle progression and cell proliferation, and eventually leads to occurrence of CML.