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ALT Dark gold and teal JBSD infographic. Penicillin-binding protein 6b, or DacD, trims peptide building blocks during E. coli cell-wall remodeling. A labelled conceptual schematic compares a small teal groove with an enlarged gold mutant groove holding a five-bead pentapeptide. CASTp pocket volumes: soluble DacD 326.1 ų; mutant DacD 693 ų; penicillin-binding protein 5 reference 960.8 ų. The larger modelled groove accommodates the peptide substrate, connecting pocket geometry to substrate recognition.

ALT Dark gold and teal JBSD infographic. Bovine serum albumin carries drugs, hormones and fatty acids in blood. An assay schematic shows glucose, methylglyoxal, glyoxal and diacetyl entering a treated-sample vial beside a native-control vial: 22 days at 37 °C. Spectroscopy showed less alpha-helical signal and more beta-sheet signatures. Dynamic light scattering gave a hydrodynamic diameter of 10.0 nm for Run 34 with 60 mg albumin, versus 8.19 nm for the 60 mg native control. Mixture composition shapes albumin damage under glycation stress. Source: Sathala and colleagues, Table 2.

ALT Dark charcoal and gold infographic: human insulin regulates blood glucose. Chondroitin sulfate A is a sugar polymer found in the extracellular matrix. A labeled assay schematic compares insulin alone with insulin plus chondroitin sulfate A at pH 2 and room temperature. Circular dichroism gives beta-sheet content of 23.8% for insulin alone and 78.8% with 1 mg/mL chondroitin sulfate A. A clear sample vessel and a cloudy treated vessel illustrate the comparison. The finding provides a room-temperature model for insulin aggregation assays. Source: Hisamuddin et al., JBSD 44:14, Table 1.

ALT Dark charcoal and gold JBSD infographic with a conceptual assay schematic of separate native rhKGF and K126E sample vials. Both were incubated at pH 5 for 24 h at 37 °C. Aggregation indices are 8.385 ± 1.0241 for native rhKGF and 7.909 ± 1.1957 for K126E (mean ± SD; n = 3). K126E has a modestly lower mean and retains cell-growth activity in MCF-7 assays. Melting temperatures are 63 °C for native and 61 °C for K126E.

ALT Dark charcoal and gold JBSD infographic with a rice plant and a labeled conceptual schematic of OsCobB plus NAD+ removing an acyl tag from an H3K9 peptide. Apparent catalytic efficiencies with NAD+ varied are 652 for glutaryl, 206 for succinyl and 118 for malonyl removal, in M⁻¹ s⁻¹ (Table 1; n = 3). Gold and teal distinguish the modifications. Glutaryl removal is most efficient among these tested acidic modifications.

ALT Dark charcoal and gold JBSD infographic. A labeled model schematic feeds apo residue descriptors into Apo-Holo and branches to backbone and side-chain mobility predictions. The dataset contains 33 apo–holo pairs and 19,891 residue instances. Reported internal classification recall is 0.8262 for backbone and 0.8570 for side chains. Recall is the fraction of observed mobile residues identified. Gold and teal distinguish the outputs. Source: Santiago Alonso-Gil, Figure 1 and Table 3.

ALT Dark charcoal and gold JBSD infographic. A labeled screening and assay schematic sends compound tokens through sievgene, DOCK 6 and AutoDock Vina to five assay wells. One gold well identifies compound 6, which inhibited human D-amino acid oxidase. The screen began with 160,000 compounds; five candidates were tested. Reported IC50: 440 ± 110 µM, with three to four independent experiments per concentration. Source: Yusuke Kato and Kiyoshi Fukui, Figures 2 and 6.

ALT Dark charcoal and gold JBSD infographic with a labeled model schematic. The first 35 and last 35 mRNA nucleotides feed ESM2, MMDO-MDPU resampling and a two-stage ensemble that predicts nine location labels. Reported Coverage is 0.9144 for EMMPREDMLsub and 0.6584 for MBSCLoc in the RNALocate comparison. Coverage is the mean fraction of known location labels recovered per sample. Gold and teal distinguish the values. Source: Luo and colleagues, Figures 1 and 8.

ALT Dark charcoal and gold JBSD infographic with a labeled assay schematic. An abstract Q1 disc branches to gold PTP1B and teal SHP2 assay plates. At 50 µM Q1, inhibition is 99.70 ± 0.05% for PTP1B and 35.26 ± 0.78% for SHP2. A lower callout gives PTP1B IC50 of 2.45 ± 0.04 µM. Source: Cao, Zhao, Zhang and Wang, Jiangnan University, Table 2.

ALT Dark charcoal and gold JBSD infographic with a labeled method schematic. Data from 35 thiazole derivatives, split into 27 training and eight test compounds, branch into HQSAR molecular-fragment and CoMSIA steric, electrostatic and hydrophobic-field models. Their maps guide nine new designs. External test-set R² is 0.817 for CoMSIA and 0.700 for HQSAR. Gold and teal distinguish the abstract model elements. Source: Zaki and colleagues, Tables 4–5 and Figure 6/Table 7.

ALT Dark charcoal and gold JBSD infographic with a labeled TSR method schematic. Three abstract points form a triangle, leading to layered geometric keys and a branching shape-comparison tree. Five benchmark datasets each contain seven classes and 20 structures per class. TSR outperforms RMSD, USR and ROSHAMBO and is slightly ahead of Phase in this comparison. Teal distinguishes schematic elements. Source: Reaux et al., Methods, Section 3.6 and Figure 10.

ALT Dark charcoal and gold JBSD infographic with a labeled assay schematic: pyrrolopyrimidine derivatives flow into a broth microdilution plate and two bacterial assay callouts. Compound 6e inhibits E. coli and compound 6h inhibits P. aeruginosa, each at a reported MIC of 50 ± 2.5 µg/mL (mean ± SD). Chloramphenicol has a mean MIC of 50 µg/mL in both strains. The study tested 14 derivatives. Bacteria and plate are conceptual illustrations. Source: Makwana et al., Table 1.

ALT Dark charcoal and gold JBSD infographic. A labeled workflow schematic splits eight papaya-associated flavonoids into bound-state MMGBSA analysis and unbinding analysis using steered molecular dynamics and umbrella sampling. Both routes lead to the same top three: neohesperidin, quercetin and myricetin, in that order. The study targets dengue-virus NS5 methyltransferase. Source: K. L. Joseph Libin and colleagues, Tables 2 and 3.

ALT Dark charcoal and gold JBSD infographic. A labeled screening schematic connects UM-4E in gold and UM-C162 in teal to Hla, SrtA, AgrA and SspA. UM-4E leads the mean docking scores across these four Staphylococcus aureus targets. Hla mean docking binding energies are −9.70 for UM-4E, −7.54 for UM-C162, −5.94 for curcumin and −5.17 for ACA, all in kcal/mol. The study used 100 docking runs per ligand–target pair. Source: Al Quwatli and colleagues, Figure 7.

ALT Black-and-gold JBSD infographic with a labeled ranking schematic. A geometric Bitopertin node branches to DAT, ECR 1.382, in gold and GlyT1, ECR 0.794, in teal. Bitopertin scores higher for DAT than GlyT1. Two smaller annotations identify NFPS_2 as first for GlyT1 at ECR 1.896 and Org 24598_2 as first for GlyT2 at ECR 1.075. ECR combines ranks from AutoDock Vina, GOLD and DockThor. Source: Nascimento and colleagues, Section 3.3 and Figure 4.

ALT Black-and-gold JBSD infographic with a labeled study-workflow schematic. A screen of 158 missense variants leads to W474C and W485R. Both variants and a separate native HEXA reference enter 500 ns molecular dynamics analysis with pyrimethamine. Reported average backbone RMSD values are approximately 0.230 nm for native, 0.224 nm for W474C and 0.264 nm for W485R. Average intermolecular hydrogen-bond counts are approximately 1.8, 3.8 and 2.2, respectively. Gold highlights show W485R has the highest average backbone RMSD and W474C the highest average hydrogen-bond count. Source: S. Ranjani et al., Table 12.

ALT Square JBSD infographic showing a conceptual Gwt1 pocket workflow that screens 9,390 compounds and identifies tivozanib and rosiglitazone. Their docking scores are −9.10 and −8.13 kcal/mol. A three-species MIC90 table lists tivozanib at 1 ± 0.5, 2 ± 1, and 1 ± 0.5 µg/mL, and rosiglitazone at 4 ± 1.5, 4 ± 2, and 1 ± 0.5 µg/mL, against C. neoformans, C. albicans, and A. fumigatus.