# | Title | Journal | Year | Citations |
---|
1 | UCSF Chimera?A visualization system for exploratory research and analysis | Journal of Computational Chemistry | 2004 | 37,095 |
2 | Semiempirical GGA-type density functional constructed with a long-range dispersion correction | Journal of Computational Chemistry | 2006 | 24,222 |
3 | Multiwfn: A multifunctional wavefunction analyzer | Journal of Computational Chemistry | 2012 | 21,818 |
4 | AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading | Journal of Computational Chemistry | 2010 | 21,573 |
5 | General atomic and molecular electronic structure system | Journal of Computational Chemistry | 1993 | 19,020 |
6 | AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility | Journal of Computational Chemistry | 2009 | 16,850 |
7 | Effect of the damping function in dispersion corrected density functional theory | Journal of Computational Chemistry | 2011 | 15,980 |
8 | Scalable molecular dynamics with NAMD | Journal of Computational Chemistry | 2005 | 15,208 |
9 | Development and testing of a general amber force field | Journal of Computational Chemistry | 2004 | 14,342 |
10 | CHARMM: A program for macromolecular energy, minimization, and dynamics calculations | Journal of Computational Chemistry | 1983 | 14,316 |
11 | GROMACS: Fast, flexible, and free | Journal of Computational Chemistry | 2005 | 13,676 |
12 | LINCS: A linear constraint solver for molecular simulations | Journal of Computational Chemistry | 1997 | 13,446 |
13 | Chemistry with ADF | Journal of Computational Chemistry | 2001 | 8,854 |
14 | The Amber biomolecular simulation programs | Journal of Computational Chemistry | 2005 | 7,742 |
15 | Optimization of parameters for semiempirical methods I. Method | Journal of Computational Chemistry | 1989 | 7,369 |
16 | CHARMM: The biomolecular simulation program | Journal of Computational Chemistry | 2009 | 7,077 |
17 | Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model | Journal of Computational Chemistry | 2003 | 6,758 |
18 | Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, Li-F | Journal of Computational Chemistry | 1983 | 6,294 |
19 | Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models | Journal of Computational Chemistry | 1992 | 6,106 |
20 | PACKMOL: A package for building initial configurations for molecular dynamics simulations | Journal of Computational Chemistry | 2009 | 5,831 |
21 | THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method | Journal of Computational Chemistry | 1992 | 5,736 |
22 | CHARMM‐GUI: A web‐based graphical user interface for CHARMM | Journal of Computational Chemistry | 2008 | 5,402 |
23 | cclib: A library for package‐independent computational chemistry algorithms | Journal of Computational Chemistry | 2008 | 4,766 |
24 | CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields | Journal of Computational Chemistry | 2010 | 4,718 |
25 | Accurate description of van der Waals complexes by density functional theory including empirical corrections | Journal of Computational Chemistry | 2004 | 4,372 |
26 | Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis | Journal of Computational Chemistry | 1990 | 4,216 |
27 | A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations | Journal of Computational Chemistry | 2003 | 4,028 |
28 | Optimization of parameters for semiempirical methods II. Applications | Journal of Computational Chemistry | 1989 | 3,741 |
29 | Macromodel?an integrated software system for modeling organic and bioorganic molecules using molecular mechanics | Journal of Computational Chemistry | 1990 | 3,727 |
30 | How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? | Journal of Computational Chemistry | 2000 | 3,725 |
31 | Optimization of equilibrium geometries and transition structures | Journal of Computational Chemistry | 1982 | 3,470 |
32 | A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 | Journal of Computational Chemistry | 2004 | 3,309 |
33 | An all atom force field for simulations of proteins and nucleic acids | Journal of Computational Chemistry | 1986 | 3,292 |
34 | Improved grid-based algorithm for Bader charge allocation | Journal of Computational Chemistry | 2007 | 3,175 |
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 | Journal of Computational Chemistry | 2004 | 3,145 |
36 | An approach to computing electrostatic charges for molecules | Journal of Computational Chemistry | 1984 | 3,071 |
37 | Atomic charges derived from semiempirical methods | Journal of Computational Chemistry | 1990 | 3,004 |
38 | Ab‐initiosimulations of materials using VASP: Density‐functional theory and beyond | Journal of Computational Chemistry | 2008 | 2,717 |
39 | Validation of the general purpose tripos 5.2 force field | Journal of Computational Chemistry | 1989 | 2,695 |
40 | Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation | Journal of Computational Chemistry | 2002 | 2,641 |
41 | CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data | Journal of Computational Chemistry | 2013 | 2,613 |
42 | Using redundant internal coordinates to optimize equilibrium geometries and transition states | Journal of Computational Chemistry | 1996 | 2,592 |
43 | Optimized Slater-type basis sets for the elements 1-118 | Journal of Computational Chemistry | 2003 | 2,314 |
44 | The role of databases in support of computational chemistry calculations | Journal of Computational Chemistry | 1996 | 2,246 |
45 | A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations | Journal of Computational Chemistry | 1990 | 2,230 |
46 | (null) | Journal of Computational Chemistry | 1996 | 2,230 |
47 | MDAnalysis: A toolkit for the analysis of molecular dynamics simulations | Journal of Computational Chemistry | 2011 | 2,201 |
48 | PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints | Journal of Computational Chemistry | 2011 | 1,978 |
49 | 6-31G* basis set for third-row atoms | Journal of Computational Chemistry | 2001 | 1,891 |
50 | A semiempirical free energy force field with charge-based desolvation | Journal of Computational Chemistry | 2007 | 1,854 |