DNCS 1.0 - Enhanced Conformational Sampling using Digital Nets Conformational Sampling
Abraham Rebairo J., D. Sam Paul, S. Satheeshkumar, Arumainathan Stephen · ChemRxiv · 2025
We developed DNCS 1.0 , a peptide modeling tool based on the Digital Nets Conformational Sampling (DNCS) method to explore the energy landscape of intrinsically disordered polypeptides (IDPs). DNCS 1.0 addresses the limitations of the DNCS method proposed earlier and can now explore the energy landscapes of longer IDPs. We provide a test case on an antimicrobial peptide and show that DNCS 1.0 can predict distinct energy basins of the polypeptide. We also show that DNCS 1.0 predicts different classes of secondary structures as well, in addition to predicting low-lying conformational ensembles. DNCS 1.0 is also integrated into OpenMM open-source molecular dynamics code.