Blog
Biomedical research blog
In-depth, evidence-led articles on computational biology, molecular modeling, and biomedical research.
How to Map Protein Aggregation Propensity with Aggrescan3D and a PDB Structure
Static Aggrescan3D 1.0.2 analysis of the official RCSB Protein Data Bank structure 2GB1 produced finite scores for all 56 residues of chain A. The minimum score was −3.5629, the maximum was 1.1983, and the arithmetic mean was −1.4135875. The highest-scoring residue was valine A:21 at 1.1983; methion
How to Align PDB Protein Structures with PyMOL and Interpret RMSD Correctly
PyMOL 3.1.0 aligned the official RCSB/PDBe 1D3Z ubiquitin NMR structure as the mobile object to the official RCSB 1UBQ X-ray ubiquitin structure as the target. The exact cmd.align return was [0.39735108613967896, 449, 5, 1.2869186401367188, 602, 381.0, 76]: refined RMSD 0.397351 Å across 449 atom pa
How to Reconstruct Ancestral DNA Sequences with ancseq and IQ-TREE
The validated workflow selected the IQ-TREE model from the supplied alignment, rooted the analysis with AVR-Mgk5GE162, reconstructed 13 ancestral records, and produced all six required final deliverables. The sorted state table contained 68,807 bytes of explicit state probabilities; intermediate IQ-
How to Annotate and Number an Antibody Light Chain with ANARCI and Kabat
ANARCI recognized a human kappa light chain spanning residues 0–106. The retained HMM score was 197.0 with an e-value of 1.6 × 10⁻61, and the assigned germlines were IGKV1-1201 and IGKJ101. Both the Kabat-numbered CSV and the HMM evidence table passed semantic validation. This result passed native e
How to Estimate Aqueous Solubility from SMILES with the ESOL Model
The model predicted logS values of −0.0424460527 for ethanol, −1.9325820263 for benzene, and −2.3143366025 for octanol. The expected ordering ethanol benzene octanol was recovered, and the output retained molecular weight, LogP, rotatable bonds, aromatic proportion, SMILES, and units. This result pa