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JournalISSN: 1093-3263

Journal of Molecular Graphics & Modelling 

Elsevier BV
About: Journal of Molecular Graphics & Modelling is an academic journal published by Elsevier BV. The journal publishes majorly in the area(s): Medicine & Docking (molecular). It has an ISSN identifier of 1093-3263. Over the lifetime, 3213 publications have been published receiving 73242 citations. The journal is also known as: Molecular graphics & modelling & Journal of molecular graphics and modelling.


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Journal ArticleDOI
TL;DR: Anautomatic algorithm of perceiving atom types that are defined in a description table, and an automatic algorithm of assigning bond types just based on atomic connectivity are presented.
Abstract: In molecular mechanics (MM) studies, atom types and/or bond types of molecules are needed to determine prior to energy calculations. We present here an automatic algorithm of perceiving atom types that are defined in a description table, and an automatic algorithm of assigning bond types just based on atomic connectivity. The algorithms have been implemented in a new module of the AMBER packages. This auxiliary module, antechamber (roughly meaning "before AMBER"), can be applied to generate necessary inputs of leap-the AMBER program to generate topologies for minimization, molecular dynamics, etc., for most organic molecules. The algorithms behind the manipulations may be useful for other molecular mechanical packages as well as applications that need to designate atom types and bond types.

4,124 citations

Journal ArticleDOI
TL;DR: It is argued that the high value of LOO q2 appears to be the necessary but not the sufficient condition for the model to have a high predictive power, which is the general property of QSAR models developed using LOO cross-validation.
Abstract: Validation is a crucial aspect of any quantitative structure-activity relationship (QSAR) modeling. This paper examines one of the most popular validation criteria, leave-one-out cross-validated R2 (LOO q2). Often, a high value of this statistical characteristic (q2 > 0.5) is considered as a proof of the high predictive ability of the model. In this paper, we show that this assumption is generally incorrect. In the case of 3D QSAR, the lack of the correlation between the high LOO q2 and the high predictive ability of a QSAR model has been established earlier [Pharm. Acta Helv. 70 (1995) 149; J. Chemomet. 10(1996)95; J. Med. Chem. 41 (1998) 2553]. In this paper, we use two-dimensional (2D) molecular descriptors and k nearest neighbors (kNN) QSAR method for the analysis of several datasets. No correlation between the values of q2 for the training set and predictive ability for the test set was found for any of the datasets. Thus, the high value of LOO q2 appears to be the necessary but not the sufficient condition for the model to have a high predictive power. We argue that this is the general property of QSAR models developed using LOO cross-validation. We emphasize that the external validation is the only way to establish a reliable QSAR model. We formulate a set of criteria for evaluation of predictive ability of QSAR models.

3,176 citations

Journal Article
TL;DR: In the laboratory, the laboratory investigates several areas, including protein-ligand docking, protein-protein docking, and complex molecular assemblies, as well as developing a number of computational tools such as molecular surfaces, phenomenological potentials, various docking and visualization programs which are used in conjunction with programs developed by others.
Abstract: One of the challenges in bio-computing is to enable the efficient use and inter-operation of a wide variety of rapidly-evolving computational methods to simulate, analyze, and understand the complex properties and interactions of molecular systems. In our laboratory we investigates several areas, including protein-ligand docking, protein-protein docking, and complex molecular assemblies. Over the years we have developed a number of computational tools such as molecular surfaces, phenomenological potentials, various docking and visualization programs which we use in conjunction with programs developed by others. The number of programs available to compute molecular properties and/or simulate molecular interactions (e.g., molecular dynamics, conformational analysis, quantum mechanics, distance geometry, docking methods, ab-initio methods) is large and growing rapidly. Moreover, these programs come in many flavors and variations, using different force fields, search techniques, algorithmic details (e.g., continuous space vs. discrete, Cartesian vs. torsional). Each variation presents its own characteristic set of advantages and limitations. These programs also tend to evolve rapidly and are usually not written as components, making it hard to get them to work together.

2,665 citations

Journal ArticleDOI
TL;DR: This work describes a heavily modified version of MolScript that has added syntax for describing complicated coloring schemes and also has new graphics commands for controlling the coloring of atoms, bonds, and molecules.
Abstract: Owing to its flexibility, MolScript has become one of the most widely used programs for generating publicationquality molecular graphics. Integration with the Raster3D package, to allow the production of photorealistic rendered images, has increased its popularity still further. However, this intensive use has shown the need for enhancement of some areas of the program, especially for controlling the coloring of atoms, bonds, and molecules. This work describes a heavily modified version of MolScript that has added syntax for describing complicated coloring schemes and also has new graphics commands. Enhancements include drawing split-bond ball-and-stick models, smoothly varying the color of molecules (color ramping), abrupt color changes within secondary structural units, and the creation of dashed bonds. Making use of these added features is simple because all MolScript syntax is still supported and one typically needs only to add a few control commands. The final section of this article suggests some uses for this modified MolScript and provides illustrative examples.

1,695 citations

Journal ArticleDOI
TL;DR: XCrySDen is a molecular and crystalline-structure visualization program, but its main function is as a property analyzer program, which can run on most UNIX platforms, without any special hardware or software requirements.
Abstract: XCrySDen is a molecular and crystalline-structure visualization program, but its main function is as a property analyzer program. It can run on most UNIX platforms, without any special hardware or software requirements. Special efforts were made to allow for appropriate display of 3D isosurfaces and 2D contours, which can be superimposed on crystalline structure and interactively rotated and manipulated. XCrySDen is also a graphical user interface for the CRYSTAL95/98 (Saunders, V. R., et al. CRYSTAL98—User’s Manual. University of Torino, Turin, Italy, 1999) ab initio program and a visualization system for the WIEN97 (Blaha, P., et al. Comput. Phys. Commun. 1990, 59, 399) ab initio program. In this article the program functions are presented with a short description of the algorithms.

1,299 citations

Performance
Metrics
No. of papers from the Journal in previous years
YearPapers
2023140
2022319
2021217
2020247
2019221
2018176