| CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2. | 0 | 0.34 | 2018 |
| Charmm-Gui Ligand Reader And Modeler For Charmm Force Field Generation Of Small Molecules | 1 | 0.37 | 2017 |
| A rapid solvent accessible surface area estimator for coarse grained molecular simulations. | 1 | 0.35 | 2017 |
| Efficient Implementation Of Constant Ph Molecular Dynamics On Modern Graphics Processors | 1 | 0.40 | 2016 |
| Parallelization And Improvements Of The Generalized Born Model With A Simple Switching Function For Modern Graphics Processors | 5 | 0.46 | 2016 |
| Coupled folding and binding with 2D Window-Exchange Umbrella Sampling. | 1 | 0.40 | 2016 |
| New paint and a new engine. | 1 | 0.34 | 2013 |
| Assessing The Quality Of Absolute Hydration Free Energies Among Charmm-Compatible Ligand Parameterization Schemes | 5 | 0.54 | 2013 |
| MATCH: An atom-typing toolset for molecular mechanics force fields. | 12 | 0.77 | 2012 |
| Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy. | 8 | 0.80 | 2011 |
| Applying efficient implicit nongeometric constraints in alchemical free energy simulations. | 1 | 0.36 | 2011 |
| Surveying implicit solvent models for estimating small molecule absolute hydration free energies. | 10 | 0.70 | 2011 |
| VIPERdb2: an enhanced and web API enabled relational database for structural virology. | 10 | 1.07 | 2009 |
| CHARMM: The biomolecular simulation program. | 373 | 24.58 | 2009 |
| De novo modeling of GPCR class A structures | 0 | 0.34 | 2009 |
| lambda-Dynamics free energy simulation methods. | 6 | 0.72 | 2009 |
| Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. | 7 | 0.80 | 2008 |
| Deprotonation By Dehydration: The Origin Of Ammonium Sensing In The Amtb Channel | 0 | 0.34 | 2007 |
| Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling | 2 | 0.36 | 2007 |
| Viperdb: A Relational Database For Structural Virology | 7 | 1.16 | 2006 |
| Metrics for Effective Resource Management in Global Computing Environments | 6 | 0.61 | 2005 |
| Detailed considerations for a balanced and broadly applicable force field: A study of substituted benzenes modeled with OPLS-AA. | 2 | 0.47 | 2005 |
| Study Of A Highly Accurate And Fast Protein-Ligand Docking Method Based On Molecular Dynamics | 2 | 0.39 | 2005 |
| Application of torsion angle molecular dynamics for efficient sampling of protein conformations. | 14 | 1.34 | 2005 |
| Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. | 64 | 10.16 | 2004 |
| Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. | 5 | 0.76 | 2004 |
| CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. | 27 | 2.66 | 2004 |
| CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. | 37 | 3.47 | 2004 |
| Characterizing and evaluating desktop grids: an empirical study | 125 | 6.84 | 2004 |
| Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. | 159 | 13.73 | 2004 |
| Studying Protein Folding On The Grid: Experiences Using Charmm On Npaci Resources Under Legion | 17 | 1.26 | 2004 |
| Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics | 4 | 0.75 | 2004 |
| Generalized born model with a simple smoothing function. | 65 | 7.11 | 2003 |
| Comparative study of several algorithms for flexible ligand docking. | 51 | 6.28 | 2003 |
| New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. | 62 | 6.53 | 2003 |
| Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. | 44 | 3.35 | 2003 |
| New analytic approximation to the standard molecular volume definition and its application to generalized born calculations - Erratum. | 0 | 0.34 | 2003 |
| Identifying native-like protein structures using physics-based potentials | 11 | 6.56 | 2002 |
| Modern protein force fields behave comparably in molecular dynamics simulations. | 11 | 3.92 | 2002 |
| Studying Protein Folding on the Grid: Experiences Using CHARMM on NPACI Resources under Legion | 12 | 1.17 | 2001 |
| Assessing energy functions for flexible docking | 14 | 1.86 | 1998 |
| Assessing search strategies for flexible docking | 9 | 2.05 | 1998 |
| Dynamic Load Balancing Algorithms for Replicated Data Molecular Dynamics | 0 | 0.34 | 1995 |
| Implementation of a data parallel, logical domain decomposition method for interparticle interactions in molecular dynamics of structured molecular fluids | 4 | 0.79 | 1994 |
| Molecular Simulations On Supercomputers | 2 | 8.12 | 1991 |
