passages.id: split_6_test_1569_passage
passages.type: progene_text
passages.text: The combined use of molecular dynamics free energy simulations to study one binding process thoroughly , followed by molecular dynamics and Poisson - Boltzmann free energy calculations to study a series of related ligands or mutations is proposed as a paradigm for protein or ligand design.The binding of Asn in an alternate , " head - to - tail " orientation observed in the homologous asparagine synthetase is analyzed , and found to be more stable than the " Asp - like " orientation studied earlier .