Quantum simulations of SARS-CoV-2 main protease Mpro enable high-quality scoring of diverse ligands von Wang, Yuhang, Murlidaran, Sruthi, Pearlman, David A.

Volltext

Structure-based approach to the prediction of disulfide bonds in proteins von Salam, Noeris K., Adzhigirey, Matvey, Sherman, Woody, Pearlman, David A.

Volltext

Predicting mutations deleterious to function in beta-lactamase TEM1 using MM-GBSA von Negron, Christopher, Pearlman, David A, Del Angel, Guillermo

Volltext

Evaluating the Molecular Mechanics Poisson−Boltzmann Surface Area Free Energy Method Using a Congeneric Series of Ligands to p38 MAP Kinase von Pearlman, David A

Volltext

Rigorous Free Energy Simulations in Virtual Screening von Cournia, Zoe, Allen, Bryce K, Beuming, Thijs, Pearlman, David A, Radak, Brian K, Sherman, Woody

Volltext

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery von Lee, Tai-Sung, Allen, Bryce K, Giese, Timothy J, Guo, Zhenyu, Li, Pengfei, Lin, Charles, McGee, T. Dwight, Pearlman, David A, Radak, Brian K, Tao, Yujun, Tsai, Hsu-Chun, Xu, Huafeng, Sherman, Woody, York, Darrin M

Volltext

Physics-based enzyme design: Predicting binding affinity and catalytic activity von Sirin, Sarah, Pearlman, David A., Sherman, Woody

Volltext

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energet... von Pearlman, David A., Case, David A., Caldwell, James W., Ross, Wilson S., Cheatham, Thomas E., DeBolt, Steve, Ferguson, David, Seibel, George, Kollman, Peter

Volltext

Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System von Pearlman, David A, Charifson, Paul S

Volltext

CONCERTS:  Dynamic Connection of Fragments as an Approach to de Novo Ligand Design von Pearlman, David A, Murcko, Mark A

Volltext

Benzene Dimer:  A Good Model for π−π Interactions in Proteins? A Comparison between the Benzene and the Toluene Dimers in the Gas Phase and in an Aqueous Solution von Chipot, Christophe, Jaffe, Richard, Maigret, Bernard, Pearlman, David A, Kollman, Peter A

Volltext

Simulation of the solvation free energies for methane, ethane, and propane and corresponding amino acid dipeptides: a critical test of the bond-PMF correction, a new set of hydroca... von Sun, Yaxiong, Spellmeyer, David, Pearlman, David A, Kollman, Peter

Volltext

Pathogenesis, prevalence, diagnosis, and management of exercise-induced bronchoconstriction: a practice parameter von Weiler, John M., MD, MBA, Anderson, Sandra D., PhD, DSc, Randolph, Christopher, MD, Bonini, Sergio, MD, Craig, Timothy J., DO, Pearlman, David S., MD, Rundell, Kenneth W., PhD, FACSM, Silvers, William S., MD, Storms, William W., MD, Bernstein, David I., MD, Blessing-Moore, Joann, MD, Cox, Linda, MD, Khan, David A., MD, Lang, David M., MD, Nicklas, Richard A., MD, Oppenheimer, John, MD, Portnoy, Jay M., MD, Schuller, Diane E., MD, Spector, Sheldon L., MD, Tilles, Stephen A., MD, Wallace, Dana, MD, Henderson, William, MD, Schwartz, Lawrence, MD, PhD, Kaufman, David, MD, Nsouli, Talal, MD, Schieken, Lawrence, MD, Rosario, Nelson, MD

Volltext

A Comparison of Alternative Approaches to Free Energy Calculations von Pearlman, David A

Volltext

FURSMASA: A new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental... von Pearlman, David A., Rao, B. Govinda, Charifson, Paul

Volltext

Improved Scoring of Ligand−Protein Interactions Using OWFEG Free Energy Grids von Pearlman, David A, Charifson, Paul S

Volltext

Comparison of mannitol and methacholine to predict exercise-induced bronchoconstriction and a clinical diagnosis of asthma von Anderson, Sandra D, Charlton, Brett, Weiler, John M, Nichols, Sara, Spector, Sheldon L, Pearlman, David S

Volltext

Free Energy Grids:  A Practical Qualitative Application of Free Energy Perturbation to Ligand Design Using the OWFEG Method von Pearlman, David A

Volltext

Quantum simulations of SARS-CoV-2 main protease M pro enable high-quality scoring of diverse ligands von Wang, Yuhang, Murlidaran, Sruthi, Pearlman, David A

Volltext

Molecular Dynamics Potential of Mean Force Calculations:  A Study of the Toluene−Ammonium π-Cation Interactions von Chipot, Christophe, Maigret, Bernard, Pearlman, David A, Kollman, Peter A

Volltext