Additional file 1 of Freeprotmap: waiting-free prediction method for protein distance map

Additional file 1: Supplementary No. 1

Additional file 3: of Critical appraisal of international guidelines for the prevention and treatment of pregnancy-associated venous thromboembolism: a systematic review

Tables S3. Data extraction template. (DOCX 14 kb

Additional file 1: of Critical appraisal of international guidelines for the screening and treatment of asymptomatic peripheral artery disease: a systematic review

Table S1. Search strategies. (DOCX 17 kb

Additional file 2: of Critical appraisal of international guidelines for the prevention and treatment of pregnancy-associated venous thromboembolism: a systematic review

Tables S2. Structure and content of the AGREE instrument. (DOCX 15 kb

Additional file 4: of Critical appraisal of international guidelines for the prevention and treatment of pregnancy-associated venous thromboembolism: a systematic review

Tables S4. Raw Data. (DOCX 16 kb

Additional file 1: of Critical appraisal of international guidelines for the prevention and treatment of pregnancy-associated venous thromboembolism: a systematic review

Table S1. Search strategies. (DOCX 15 kb

Identification of Thyroid Hormone Disruptors among HO-PBDEs: <i>In Vitro</i> Investigations and Coregulator Involved Simulations

Some hydroxylated polybrominated diphenyl ethers (HO-PBDEs), that have been widely detected in the environment and tissues of humans and wildlife, bind to thyroid hormone (TH) receptor (TR) and can disrupt functioning of systems modulated by the TR. However, mechanisms of TH disrupting effects are still equivocal. Here, disruption of functions of TH modulated pathways by HO-PBDEs was evaluated by assays of competitive binding, coactivator recruitment, and proliferation of GH3 cells. <i>In silico</i> simulations considering effects of coregulators were carried out to investigate molecular mechanisms and to predict potencies for disrupting functions of the TH. Some HO-PBDEs were able to bind to TR with moderate affinities but were not agonists. In GH3 proliferation assays, 13 out of 16 HO-PBDEs were antagonists for the TH. <i>In silico</i> simulations of molecular dynamics revealed that coregulators were essential for identification of TH disruptors. Among HO-PBDEs, binding of passive antagonists induced repositioning of H12, blocking AF-2 (transactivation function 2) and preventing recruitment of the coactivator. Binding of active antagonists exposed the coregulator binding site, which tended to bind to the corepressor rather than the coactivator. By considering both passive and active antagonisms, anti-TH potencies of HO-PBDEs could be predicted from free energy of binding

Additional file 2: of Critical appraisal of international guidelines for the screening and treatment of asymptomatic peripheral artery disease: a systematic review

Table S2. Structure and content of the AGREE instrument. (DOCX 15 kb

Data_Sheet_1_Genome-Wide Identification and Expression Analysis of the R2R3-MYB Transcription Factor Family Revealed Their Potential Roles in the Flowering Process in Longan (Dimocarpus longan).docx

Longan (Dimocarpus longan Lour.) is a productive fruit crop with high nutritional and medical value in tropical and subtropical regions. The MYB gene family is one of the most widespread plant transcription factor (TF) families participating in the flowering regulation. However, little is known about the MYB TFs involved in the flowering process in longan and its regulatory network. In this study, a total of 119 DlR2R3-MYB genes were identified in the longan genome and were phylogenetically grouped into 28 subgroups. The groupings were supported by highly conserved gene structures and motif composition of DlR2R3-MYB genes in each subgroup. Collinearity analysis demonstrated that segmental replications played a more crucial role in the expansion of the DlR2R3-MYB gene family compared to tandem duplications, and all tandem/segmental duplication gene pairs have evolved under purifying selection. Interspecies synteny analysis among longan and five representative species implied the occurrence of gene duplication events was one of the reasons contributing to functional differentiation among species. RNA-seq data from various tissues showed DlR2R3-MYB genes displayed tissue-preferential expression patterns. The pathway of flower development was enriched with six DlR2R3-MYB genes. Cis-acting element prediction revealed the putative functions of DlR2R3-MYB genes were related to the plant development, phytohormones, and environmental stresses. Notably, the orthologous counterparts between Arabidopsis and longan R2R3-MYB members tended to play conserved roles in the flowering regulation and stress responses. Transcriptome profiling on off-season flower induction (FI) by KClO3 indicated two up-regulated and four down-regulated DlR2R3-MYB genes involved in the response to KClO3 treatment compared with control groups. Additionally, qRT-PCR confirmed certain genes exhibited high expression in flowers/flower buds. Subcellular localization experiments revealed that three predicted flowering-associated MYB proteins were localized in the nucleus. Future functional studies on these potential candidate genes involved in the flowering development could further the understanding of the flowering regulation mechanism.</p

Structures of Endocrine-Disrupting Chemicals Correlate with the Activation of 12 Classic Nuclear Receptors

Endocrine-disrupting chemicals (EDCs) can inadvertently interact with 12 classic nuclear receptors (NRs) that disrupt the endocrine system and cause adverse effects. There is no widely accepted understanding about what structural features make thousands of EDCs able to activate different NRs as well as how these structural features exert their functions and induce different outcomes at the cellular level. This paper applies the hierarchical characteristic fragment methodology and high-throughput screening molecular docking to comprehensively explore the structural and functional features of EDCs for the 12 NRs based on more than 7000 chemicals from curated datasets. EDCs share three levels of key fragments. The primary and secondary fragments are associated with the binding of EDCs to four groups of receptors: steroidal nuclear receptors (SNRs, including androgen, estrogen, glucocorticoid, mineralocorticoid, and progesterone), retinoic acid receptors, thyroid hormone receptors, and vitamin D receptors. The tertiary fragments determine the activity type by interacting with two key locations in the ligand-binding domains of NRs (N–H5–H3–C and N–H7–H11–C for SNRs and N–H5–H5′–H2′–H3–C and N–H6′–H11–C for non-SNRs). The resulting compiled structural fragments of EDCs together with elucidated compound NR binding modes provide a framework for understanding the interactions between EDCs and NRs, facilitating faster and more accurate screening of EDCs for multiple NRs in the future