| # | Title | Journal | Year | Citations |
|---|
| 1 | VMD: Visual molecular dynamics | Journal of Molecular Graphics | 1996 | 46,937 |
| 2 | MOLMOL: A program for display and analysis of macromolecular structures | Journal of Molecular Graphics | 1996 | 6,760 |
| 3 | WHAT IF: A molecular modeling and drug design program | Journal of Molecular Graphics | 1990 | 3,213 |
| 4 | DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package | Journal of Molecular Graphics | 1996 | 2,029 |
| 5 | HOLE: A program for the analysis of the pore dimensions of ion channel structural models | Journal of Molecular Graphics | 1996 | 1,425 |
| 6 | SETOR: Hardware-lighted three-dimensional solid model representations of macromolecules | Journal of Molecular Graphics | 1993 | 1,265 |
| 7 | The MIDAS display system | Journal of Molecular Graphics | 1988 | 914 |
| 8 | SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions | Journal of Molecular Graphics | 1995 | 870 |
| 9 | A fast algorithm for rendering space-filling molecule pictures | Journal of Molecular Graphics | 1988 | 575 |
| 10 | The molecular surface package | Journal of Molecular Graphics | 1993 | 548 |
| 11 | A visual protein crystallographic software system for X11/Xview | Journal of Molecular Graphics | 1992 | 533 |
| 12 | Ribbon models of macromolecules | Journal of Molecular Graphics | 1987 | 483 |
| 13 | A graphics program for the analysis and display of molecular dynamics trajectories | Journal of Molecular Graphics | 1992 | 448 |
| 14 | Targeted molecular dynamics: A new approach for searching pathways of conformational transitions | Journal of Molecular Graphics | 1994 | 424 |
| 15 | CHAIN — A crystallographic modeling program | Journal of Molecular Graphics | 1988 | 331 |
| 16 | POCKET: A computer graphies method for identifying and displaying protein cavities and their surrounding amino acids | Journal of Molecular Graphics | 1992 | 272 |
| 17 | Interactive program for visualization and modelling of proteins, nucleic acids and small molecules | Journal of Molecular Graphics | 1986 | 146 |
| 18 | Algorithm for ribbon models of proteins | Journal of Molecular Graphics | 1986 | 134 |
| 19 | Conic: A fast renderer for spacefilling molecules with shadows | Journal of Molecular Graphics | 1991 | 134 |
| 20 | TOM: a FRODO subpackage for protein-ligand fitting with interactive energy minimization | Journal of Molecular Graphics | 1987 | 133 |
| 21 | Measurement of protein surface shape by solid angles | Journal of Molecular Graphics | 1986 | 118 |
| 22 | 3D molecular lipophilicity potential profiles: a new tool in molecular modeling | Journal of Molecular Graphics | 1988 | 116 |
| 23 | BRAGI: A comprehensive protein modeling program system | Journal of Molecular Graphics | 1988 | 101 |
| 24 | Pharmacological distribution diagrams: A tool for de novo drug design | Journal of Molecular Graphics | 1996 | 101 |
| 25 | A very fast program for visualizing protein surfaces, channels and cavities | Journal of Molecular Graphics | 1989 | 99 |
| 26 | Molecular volumes and surfaces of biomacromolecules via GEPOL: A fast and efficient algorithm | Journal of Molecular Graphics | 1990 | 98 |
| 27 | An ellipsoidal approximation of protein shape | Journal of Molecular Graphics | 1983 | 95 |
| 28 | Automated site-directed drug design using molecular lattices | Journal of Molecular Graphics | 1992 | 95 |
| 29 | Estimating and representing hydrophobicity potential | Journal of Molecular Graphics | 1988 | 93 |
| 30 | A 3D model of the peripheral benzodiazepine receptor and its implication in intra mitochondrial cholesterol transport | Journal of Molecular Graphics | 1993 | 91 |
| 31 | Molecular recognition: 3D surface structure comparison by gnomonic projection | Journal of Molecular Graphics | 1987 | 90 |
| 32 | MOLView: A program for analyzing and displaying atomic structures on the Macintosh personal computer | Journal of Molecular Graphics | 1995 | 86 |
| 33 | Pharmacophoric pattern matching in files of 3-D chemical structures: selection of interatomic distance screens | Journal of Molecular Graphics | 1986 | 84 |
| 34 | Molecular recognition: designed crystalline inclusion complexes of carboxylic hosts | Journal of Molecular Graphics | 1989 | 82 |
| 35 | Molecular recognition using a binary genetic search algorithm | Journal of Molecular Graphics | 1993 | 82 |
| 36 | Chaos game representation of protein structures | Journal of Molecular Graphics | 1994 | 81 |
| 37 | Description of molecular surface shape using Fourier descriptors | Journal of Molecular Graphics | 1988 | 80 |
| 38 | Pharmacophoric pattern matching in files of 3D chemical structures: comparison of geometric searching algorithms | Journal of Molecular Graphics | 1987 | 79 |
| 39 | CRYStallize: A crystallographic symmetry display and handling subpackage in TOM/FRODO | Journal of Molecular Graphics | 1990 | 78 |
| 40 | Pharmacophoric pattern matching in files of 3D chemical structures: evaluation of search performance | Journal of Molecular Graphics | 1987 | 74 |
| 41 | Molecular recognition: optimized searching through rotational 3-space for pattern matches on molecular surfaces | Journal of Molecular Graphics | 1987 | 73 |
| 42 | PREDITOP: A program for antigenicity prediction | Journal of Molecular Graphics | 1993 | 72 |
| 43 | Texture mapping: A new tool for molecular graphics | Journal of Molecular Graphics | 1994 | 68 |
| 44 | DRAWNA: A program for drawing schematic views of nucleic acids | Journal of Molecular Graphics | 1994 | 66 |
| 45 | Predicting metabolic pathways by logic programming | Journal of Molecular Graphics | 1988 | 65 |
| 46 | PEANUT: Computer graphics program to represent atomic displacement parameters | Journal of Molecular Graphics | 1990 | 64 |
| 47 | Modeling cytochrome P450 14α demethylase (Candida albicans) from P450cam | Journal of Molecular Graphics | 1994 | 64 |
| 48 | Modeling polysaccharides: Present status and challenges | Journal of Molecular Graphics | 1996 | 64 |
| 49 | Depth-buffer algorithms for molecular modelling | Journal of Molecular Graphics | 1985 | 62 |
| 50 | Novel method for the display of multivariate data using neural networks | Journal of Molecular Graphics | 1991 | 61 |
