3 papers
q-bio.BM2026
Bayesian Learning of Distance Metrics Beyond RMSD for Biomolecule Alignment, Clustering, and Domain Identification
Saumyak Mukherjee, Gerhard Hummer
Root-mean-square deviation (RMSD) is the standard metric of structural comparison in molecular dynamics (MD) simulations. In its conventional form, RMSD assigns equal weight to all…
cond-mat.soft2025
Surface Induced Frustration of Inherent Dipolar Order in Nanoconfined Water
Sayantan Mondal, Saumyak Mukherjee, Biman Bagchi
Surface effects could play a dominant role in modifying the natural liquid order. In some cases, the effects of the surface interactions can propagate inwards, and even can interfe…
q-bio.BM2025
BEER: Biochemical Estimator and Explorer of Residues -- A Comprehensive Software Suite for Protein Sequence Analysis
Saumyak Mukherjee
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or…