articles
- Molecular dynamics analysis of Mg2+ -dependent cleavage of a pistol ribozyme reveals a fail-safe secondary ion for catalysis 2020
- AutoGridFR: Improvements on AutoDock affinity maps and associated software tools 2019
- "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics. 38:1321-1331. 2017
- Are induced fit protein conformational changes caused by ligand-binding predictable? A molecular dynamics investigation. 38:1229-1237. 2017
- Molecular simulations to delineate functional conformational transitions in the HCV polymerase. 38:1125-1137. 2017
- Optimal allosteric stabilization sites using contact stabilization analysis. 38:1138-1146. 2017
- Residue-centric modeling and design of saccharide and glycoconjugate structures. 38:276-287. 2017
- Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation. 38:1438-1446. 2017
- Model parameters for simulation of physiological lipids. 37:1112-1118. 2016
- Development and use of an atomistic CHARMM-based forcefield for peptoid simulation. 35:360-370. 2014
- Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. 33:1880-1891. 2012
- Analyzing the robustness of the MM/PBSA free energy calculation method: application to DNA conformational transitions. 32:1431-1440. 2011
- CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. 31:671-690. 2010
- AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. 31:455-461. 2010
- AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. 30:2785-2791. 2009
- Additive empirical force field for hexopyranose monosaccharides. 29:2543-2564. 2008
- Empirical entropic contributions in computational docking: evaluation in APS reductase complexes. 29:1753-1761. 2008
- Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface. 28:1883-1892. 2007
- A semiempirical free energy force field with charge-based desolvation. 28:1145-1152. 2007
- DFT calculations of 57Fe Mossbauer isomer shifts and quadrupole splittings for iron complexes in polar dielectric media: applications to methane monooxygenase and ribonucleotide reductase. 27:1292-1306. 2006
- Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. 25:1005-1014. 2004
- Catalysis on the coastline: Theozyme, molecular dynamics, and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole. 24:98-110. 2003
- Detailed analysis of grid-based molecular docking: a case study of CDOCKER - A CHARMm-based MD docking algorithm. 24:1549-1562. 2003
- Icff: A new method to incorporate implicit flexibility into an internal coordinate force field. 24:254-265. 2003
- Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy. 23:214-221. 2002
- Identifying native-like protein structures using physics-based potentials. 23:147-160. 2002
- Assessing energy functions for flexible docking. 19:1612-1622. 1998
- Assessing search strategies for flexible docking. 19:1623-1631. 1998
- Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. 19:1639-1662. 1998
- Garant - a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. 18:139-149. 1997
- Lattice modeling: accuracy of energy calculations. 17:1025-1032. 1996
- The ellipsoid algorithm as a method for the determination of polypeptide conformations from experimental distance constraints and energy minimization. 8:132-141. 1987