Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

• Published in: Journal of computational chemistry Vol. 32; no. 5; pp. 866 - 877
• Main Authors: Hou, Tingjun, Wang, Junmei, Li, Youyong, Wang, Wei
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 15.04.2011; Wiley Subscription Services, Inc
• Subjects: Accuracy; Approximation; binding free energy; Binding sites; Catalytic Domain; generalized Born; Ligands; MM/GBSA; MM/PBSA; Models, Molecular; molecular docking; Molecular Dynamics Simulation; Poisson Boltzmann; Proteins; Proteins - chemistry; Software; Surface Properties; Technological change; Thermodynamics

In molecular docking, it is challenging to develop a scoring function that is accurate to conduct high-throughput screenings. Most scoring functions implemented in popular docking software packages were developed with many approximations for computational efficiency, which sacrifices the accuracy of...