Top publications in computational chemistry 1–100 of 54,702 results
Publications Citations  
1
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations (1983) 3618
2
UCSF Chimera - A visualization system for exploratory research and analysis (2004) 1748
3
General atomic and molecular electronic structure system (1993) 1623
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function (1998) 1524
5
Optimization of parameters for semiempirical methods I. Method (1989) 1120
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Scalable molecular dynamics with NAMD (2005) 1115
7
LINCS: A linear constraint solver for molecular simulations (1997) 1001
8
The influence of polarization functions on molecular orbital hydrogenation energies (1973) 965
9
An all atom force field for simulations of proteins and nucleic acids (1986) 714
10
GROMACS: Fast, flexible, and free (2005) 656
11
The Amber biomolecular simulation programs (2005) 649
12
Macromodel?an integrated software system for modeling organic and bioorganic molecules using molecular mechanics (1990) 579
13
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? (2000) 562
14
Optimization of parameters for semiempirical methods II. Applications (1989) 485
15
Karplus M: CHARMM: a program for macromolecular energy minimization and dynamics calculations (1983) 456
16
Chemistry with ADF (2001) 451
17
Development and testing of a general amber force field (2004) 436
18
MOPAC: A semiempirical molecular orbital program (1990) 407
19
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method (1992) 396
20
Validation of the general purpose tripos 5.2 force field (1989) 394
21
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models (1992) 388
22
Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, LiF (1983) 385
23
A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation (1991) 373
24
Energy-adjusted ab initio pseudopotentials for the second and third row transition elements (1990) 372
25
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations (2003) 357
26
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 (1996) 338
27
Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis (1990) 328
28
GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation (2008) 328
29
Chemical Similarity Searching (1998) 313
30
Atomic charges derived from semiempirical methods (1990) 299
31
ZINC - A Free Database of Commercially Available Compounds for Virtual Screening (2005) 293
32
Calculating the electrostatic potential of molecules in solution: Method and error assessment (1988) 291
33
An approach to computing electrostatic charges for molecules (1984) 280
34
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules (1988) 264
35
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 (2004) 258
36
ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation (1994) 255
37
Optimization of equilibrium geometries and transition structures (1982) 252
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All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data (2000) 250
39
Use of StructureActivity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection (1996) 236
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AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions (1981) 235
41
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations (1990) 230
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Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model (2003) 228
43
Towards an order- (1998) 222
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Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 (1996) 221
45
Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules (1998) 216
46
Application of Genetic Function Approximation to Quantitative StructureActivity Relationships and Quantitative Structure-Property Relationships (1994) 215
47
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure (1994) 213
48
Using redundant internal coordinates to optimize equilibrium geometries and transition states (1996) 211
49
An intermediate neglect of differential overlap technique for spectroscopy: Pyrrole and the azines (1973) 210
50
Analysis of the geometry of the hydroxymethyl radical by the “different hybrids for different spins” natural bond orbital procedure (1988) 205
51
Semiempirical GGA-type density functional constructed with a long-range dispersion correction (2006) 203
52
Molden: a pre- and post-processing program for molecular and electronic structures (2000) 202
53
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 (2004) 198
54
Bonded-atom fragments for describing molecular charge densities (1977) 192
55
IMOMM: A New Integrated Ab Initio + Molecular Mechanics Geometry Optimization Scheme of Equilibrium Structures and Transition States (1995) 190
56
Automated docking with grid-based energy evaluation (1992) 187
57
A semiempirical free energy force field with charge-based desolvation (2007) 186
58
CHARMM: the biomolecular simulation program (2009) 181
59
Accurate description of van der Waals complexes by density functional theory including empirical corrections (2004) 179
60
Optimization of parameters for semiempirical methods 1 (1989) 176
61
The computer program LUDI: A new method for the de novo design of enzyme inhibitors (1992) 173
62
Empirical force fields for biological macromolecules: Overview and issues (2004) 169
63
Hondo: a general atomic and molecular electronic structure system (1993) 163
64
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures (1993) 162
65
Virtual computational chemistry laboratory - design and description (2005) 160
66
Molecular Complexity and Its Impact on the Probability of Finding Leads for Drug Discovery (2001) 158
67
Calculation of the average properties of atoms in molecules. II (1982) 157
68
A new energy decomposition scheme for molecular interactions within the Hartree-Fock approximation (1976) 156
69
Rapid grid-based 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
70
Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions (2006) 148
71
Is There a Difference between Leads and Drugs? A Historical Perspective (2001) 147
72
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes (1997) 145
73
IMOMM: A new integratedab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states (1995) 145
74
An algorithm for the location of transition states (1986) 139
75
New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation (1994) 138
76
Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics (1989) 137
77
Critical evaluation of search algorithms for automated molecular docking and database screening (1997) 137
78
Merck molecular force field (1996) 135
79
AIM2000 (2001) 133
80
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases (2001) 130
81
Density matrix averaged atomic natural orbital (ANO) basis sets for correlated molecular wave functions (1990) 129
82
Atom pairs as molecular features in structure-activity studies: definition and applications (1985) 128
83
An efficient newton-like method for molecular mechanics energy minimization of large molecules (1987) 128
84
Generalized born model with a simple smoothing function (2003) 128
85
Modification of the integral isoconversional method to account for variation in the activation energy (2001) 127
86
PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules (1996) 126
87
Accelerating molecular modeling applications with graphics processors (2007) 124
88
Geometry optimization of molecular structures in solution by the polarizable continuum model (1998) 124
89
The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding (1997) 121
90
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution (2000) 121
91
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
92
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular. interactions (1996) 119
93
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 M06-class functionals and 12 other functionals (2008) 118
94
Molecular docking using shape descriptors (1992) 116
95
Atomic Physicochemical Parameters for Three-Dimensional Structure-Directed Quantitative StructureActivity Relationships I. Partition Coefficients as a Measure of Hydrophobicity (1986) 116
96
Configuration interaction calculations on the nitrogen molecule (1974) 116
97
Atomic charges derived from electrostatic potentials: A detailed study (1987) 116
98
The Problem of Overfitting (2004) 116
99
MMFF VI. MMFF94s option for energy minimization studies (1999) 116
100
Porphyrins (1966) 114