# | Title | Journal | Year | Citations |
---|
1 | Automatic atom type and bond type perception in molecular mechanical calculations | Journal of Molecular Graphics and Modelling | 2006 | 4,173 |
2 | Beware of q2! | Journal of Molecular Graphics and Modelling | 2002 | 3,216 |
3 | Intrinsically disordered protein | Journal of Molecular Graphics and Modelling | 2001 | 2,005 |
4 | Python: a programming language for software integration and development | Journal of Molecular Graphics and Modelling | 1999 | 1,586 |
5 | An extensively modified version of MolScript that includes greatly enhanced coloring capabilities | Journal of Molecular Graphics and Modelling | 1997 | 1,533 |
6 | Quantitative analysis of molecular surface based on improved Marching Tetrahedra algorithm | Journal of Molecular Graphics and Modelling | 2012 | 1,449 |
7 | XCrySDen—a new program for displaying crystalline structures and electron densities | Journal of Molecular Graphics and Modelling | 1999 | 1,315 |
8 | Macmolplt: a graphical user interface for GAMESS | Journal of Molecular Graphics and Modelling | 1998 | 981 |
9 | LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites | Journal of Molecular Graphics and Modelling | 2003 | 858 |
10 | MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology | Journal of Molecular Graphics and Modelling | 2004 | 807 |
11 | LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins | Journal of Molecular Graphics and Modelling | 1997 | 589 |
12 | Visualization of solvation structures in liquid mixtures | Journal of Molecular Graphics and Modelling | 1997 | 414 |
13 | VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs | Journal of Molecular Graphics and Modelling | 2002 | 404 |
14 | Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods | Journal of Molecular Graphics and Modelling | 2010 | 390 |
15 | Consensus scoring for ligand/protein interactions | Journal of Molecular Graphics and Modelling | 2002 | 376 |
16 | Fast empirical pKa prediction by Ewald summation | Journal of Molecular Graphics and Modelling | 2006 | 349 |
17 | LigScore: a novel scoring function for predicting binding affinities | Journal of Molecular Graphics and Modelling | 2005 | 345 |
18 | GPU-accelerated molecular modeling coming of age | Journal of Molecular Graphics and Modelling | 2010 | 336 |
19 | Steered molecular dynamics investigations of protein function | Journal of Molecular Graphics and Modelling | 2001 | 327 |
20 | A widely applicable set of descriptors | Journal of Molecular Graphics and Modelling | 2000 | 313 |
21 | Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations | Journal of Molecular Graphics and Modelling | 2004 | 307 |
22 | Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case | Journal of Molecular Graphics and Modelling | 2009 | 298 |
23 | Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems | Journal of Molecular Graphics and Modelling | 1998 | 291 |
24 | Assessing the performance of OMEGA with respect to retrieving bioactive conformations | Journal of Molecular Graphics and Modelling | 2003 | 281 |
25 | Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50 | Journal of Molecular Graphics and Modelling | 2002 | 280 |
26 | The importance of the domain of applicability in QSAR modeling | Journal of Molecular Graphics and Modelling | 2008 | 256 |
27 | eHiTS: A new fast, exhaustive flexible ligand docking system | Journal of Molecular Graphics and Modelling | 2007 | 222 |
28 | Statistical external validation and consensus modeling: A QSPR case study for Koc prediction | Journal of Molecular Graphics and Modelling | 2007 | 221 |
29 | Qmol: a program for molecular visualization on Windows-based PCs | Journal of Molecular Graphics and Modelling | 2001 | 208 |
30 | The connectivity index 25 years after | Journal of Molecular Graphics and Modelling | 2001 | 198 |
31 | BINANA: A novel algorithm for ligand-binding characterization | Journal of Molecular Graphics and Modelling | 2011 | 197 |
32 | POVME: An algorithm for measuring binding-pocket volumes | Journal of Molecular Graphics and Modelling | 2011 | 186 |
33 | Comparison of algorithms for dissimilarity-based compound selection | Journal of Molecular Graphics and Modelling | 1997 | 174 |
34 | Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand–protein inverse docking approach | Journal of Molecular Graphics and Modelling | 2001 | 135 |
35 | Crystallographic autostereograms | Journal of Molecular Graphics and Modelling | 2001 | 135 |
36 | Characterization and comparison of pore landscapes in crystalline porous materials | Journal of Molecular Graphics and Modelling | 2013 | 130 |
37 | Quaternions in molecular modeling | Journal of Molecular Graphics and Modelling | 2007 | 129 |
38 | How do carbon nanotubes serve as carriers for gemcitabine transport in a drug delivery system? | Journal of Molecular Graphics and Modelling | 2011 | 125 |
39 | Hexagonal boron nitride nanosheet as novel drug delivery system for anticancer drugs: Insights from DFT calculations and molecular dynamics simulations | Journal of Molecular Graphics and Modelling | 2019 | 123 |
40 | The whey acidic protein family: a new signature motif and three-dimensional structure by comparative modeling | Journal of Molecular Graphics and Modelling | 1999 | 121 |
41 | 3D-MoRSE descriptors explained | Journal of Molecular Graphics and Modelling | 2014 | 121 |
42 | COMPARE: a web accessible tool for investigating mechanisms of cell growth inhibition | Journal of Molecular Graphics and Modelling | 2002 | 118 |
43 | Elastic models of conformational transitions in macromolecules | Journal of Molecular Graphics and Modelling | 2002 | 117 |
44 | Molecular scaffold-based design and comparison of combinatorial libraries focused on the ATP-binding site of protein kinases | Journal of Molecular Graphics and Modelling | 1999 | 113 |
45 | Identifying protein folding cores from the evolution of flexible regions during unfolding | Journal of Molecular Graphics and Modelling | 2002 | 113 |
46 | Protein flexibility and dynamics using constraint theory | Journal of Molecular Graphics and Modelling | 2001 | 109 |
47 | A possible model of benzimidazole binding to β-tubulin disclosed by invoking an inter-domain movement | Journal of Molecular Graphics and Modelling | 2004 | 106 |
48 | Vibrational analysis and formation mechanism of typical deep eutectic solvents: An experimental and theoretical study | Journal of Molecular Graphics and Modelling | 2016 | 105 |
49 | Prediction of passive blood–brain partitioning: Straightforward and effective classification models based on in silico derived physicochemical descriptors | Journal of Molecular Graphics and Modelling | 2010 | 104 |
50 | MANIP: an interactive tool for modelling RNA | Journal of Molecular Graphics and Modelling | 1998 | 103 |