
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations (1983)

3618


UCSF Chimera  A visualization system for exploratory research and analysis (2004)

1748


General atomic and molecular electronic structure system (1993)

1623


Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function (1998)

1524


Optimization of parameters for semiempirical methods I. Method (1989)

1120


Scalable molecular dynamics with NAMD (2005)

1115


LINCS: A linear constraint solver for molecular simulations (1997)

1001


The influence of polarization functions on molecular orbital hydrogenation energies (1973)

965


An all atom force field for simulations of proteins and nucleic acids (1986)

714


GROMACS: Fast, flexible, and free (2005)

656


The Amber biomolecular simulation programs (2005)

649


Macromodel?an integrated software system for modeling organic and bioorganic molecules using molecular mechanics (1990)

579


How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? (2000)

562


Optimization of parameters for semiempirical methods II. Applications (1989)

485


Karplus M: CHARMM: a program for macromolecular energy minimization and dynamics calculations (1983)

456


Chemistry with ADF (2001)

451


Development and testing of a general amber force field (2004)

436


MOPAC: A semiempirical molecular orbital program (1990)

407


THE weighted histogram analysis method for freeenergy calculations on biomolecules. I. The method (1992)

396


Validation of the general purpose tripos 5.2 force field (1989)

394


Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models (1992)

388


Efficient diffuse functionaugmented basis sets for anion calculations. III. The 321+G basis set for firstrow elements, LiF (1983)

385


A rapid finite difference algorithm, utilizing successive overrelaxation to solve the PoissonBoltzmann equation (1991)

373


Energyadjusted ab initio pseudopotentials for the second and third row transition elements (1990)

372


A pointcharge force field for molecular mechanics simulations of proteins based on condensedphase quantum mechanical calculations (2003)

357


Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 (1996)

338


Determining atomcentered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis (1990)

328


GROMACS 4: Algorithms for Highly Efficient, LoadBalanced, and Scalable Molecular Simulation (2008)

328


Chemical Similarity Searching (1998)

313


Atomic charges derived from semiempirical methods (1990)

299


ZINC  A Free Database of Commercially Available Compounds for Virtual Screening (2005)

293


Calculating the electrostatic potential of molecules in solution: Method and error assessment (1988)

291


An approach to computing electrostatic charges for molecules (1984)

280


SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules (1988)

264


Extending the treatment of backbone energetics in protein force fields: Limitations of gasphase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations (2004)

258


ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation (1994)

255


Optimization of equilibrium geometries and transition structures (1982)

252


Allatom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data (2000)

250


Use of StructureActivity Data To Compare StructureBased Clustering Methods and Descriptors for Use in Compound Selection (1996)

236


AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions (1981)

235


A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations (1990)

230


Energies, structures, and electronic properties of molecules in solution with the CPCM solvation model (2003)

228


Towards an order (1998)

222


Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 (1996)

221


Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules (1998)

216


Application of Genetic Function Approximation to Quantitative StructureActivity Relationships and Quantitative StructureProperty Relationships (1994)

215


The development of a simple empirical scoring function to estimate the binding constant for a proteinligand complex of known threedimensional structure (1994)

213


Using redundant internal coordinates to optimize equilibrium geometries and transition states (1996)

211


An intermediate neglect of differential overlap technique for spectroscopy: Pyrrole and the azines (1973)

210


Analysis of the geometry of the hydroxymethyl radical by the “different hybrids for different spins” natural bond orbital procedure (1988)

205


Semiempirical GGAtype density functional constructed with a longrange dispersion correction (2006)

203


Molden: a pre and postprocessing program for molecular and electronic structures (2000)

202


A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS forcefield parameter sets 53A5 and 53A6 (2004)

198


Bondedatom fragments for describing molecular charge densities (1977)

192


IMOMM: A New Integrated Ab Initio + Molecular Mechanics Geometry Optimization Scheme of Equilibrium Structures and Transition States (1995)

190


Automated docking with gridbased energy evaluation (1992)

187


A semiempirical free energy force field with chargebased desolvation (2007)

186


CHARMM: the biomolecular simulation program (2009)

181


Accurate description of van der Waals complexes by density functional theory including empirical corrections (2004)

179


Optimization of parameters for semiempirical methods 1 (1989)

176


The computer program LUDI: A new method for the de novo design of enzyme inhibitors (1992)

173


Empirical force fields for biological macromolecules: Overview and issues (2004)

169


Hondo: a general atomic and molecular electronic structure system (1993)

163


Boltzmann's principle, knowledgebased mean fields and protein folding. An approach to the computational determination of protein structures (1993)

162


Virtual computational chemistry laboratory  design and description (2005)

160


Molecular Complexity and Its Impact on the Probability of Finding Leads for Drug Discovery (2001)

158


Calculation of the average properties of atoms in molecules. II (1982)

157


A new energy decomposition scheme for molecular interactions within the HartreeFock approximation (1976)

156


Rapid gridbased construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects (2002)

152


Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions (2006)

148


Is There a Difference between Leads and Drugs? A Historical Perspective (2001)

147


Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes (1997)

145


IMOMM: A new integratedab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states (1995)

145


An algorithm for the location of transition states (1986)

139


New SphericalCutoff Methods for LongRange Forces in Macromolecular Simulation (1994)

138


Atomic physicochemical parameters for three dimensional structure directed quantitative structureactivity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics (1989)

137


Critical evaluation of search algorithms for automated molecular docking and database screening (1997)

137


Merck molecular force field (1996)

135


AIM2000 (2001)

133


DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases (2001)

130


Density matrix averaged atomic natural orbital (ANO) basis sets for correlated molecular wave functions (1990)

129


Atom pairs as molecular features in structureactivity studies: definition and applications (1985)

128


An efficient newtonlike method for molecular mechanics energy minimization of large molecules (1987)

128


Generalized born model with a simple smoothing function (2003)

128


Modification of the integral isoconversional method to account for variation in the activation energy (2001)

127


PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules (1996)

126


Accelerating molecular modeling applications with graphics processors (2007)

124


Geometry optimization of molecular structures in solution by the polarizable continuum model (1998)

124


The Information Content of 2D and 3D Structural Descriptors Relevant to LigandReceptor Binding (1997)

121


Allatom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution (2000)

121


The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level (1999)

119


Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular. interactions (1996)

119


The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06class functionals and 12 other functionals (2008)

118


Molecular docking using shape descriptors (1992)

116


Atomic Physicochemical Parameters for ThreeDimensional StructureDirected Quantitative StructureActivity Relationships I. Partition Coefficients as a Measure of Hydrophobicity (1986)

116


Configuration interaction calculations on the nitrogen molecule (1974)

116


Atomic charges derived from electrostatic potentials: A detailed study (1987)

116


The Problem of Overfitting (2004)

116


MMFF VI. MMFF94s option for energy minimization studies (1999)

116


Porphyrins (1966)

114
