Prediction of SAMPL3 host–guest binding affinities: evaluating the accuracy of generalized force-fields

New Ultrahigh Affinity Host−Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations

(2011) Sarvin Moghaddam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Energy Computation Paradox and ab initio Protein Folding

(2011) John C. Faver et al.   PLoS One

Limits of Free Energy Computation for Protein−Ligand Interactions

(2010) Kenneth M. Merz   Journal of Chemical Theory and Computation

Theory of Free Energy and Entropy in Noncovalent Binding

(2009) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions

(2009) Robert S. Paton et al.   Journal of Chemical Information and Modeling

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlatedab InitioQuantum Chemical and Empirical Potential Procedures

(2009) Karel Berka et al.   Journal of Chemical Theory and Computation

Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes

(2009) Jan Řezáč et al.   Journal of Chemical Theory and Computation

Host−Guest Complexes with Protein−Ligand-like Affinities: Computational Analysis and Design

(2009) Sarvin Moghaddam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation