Shoichet B, Bodian D, Kuntz I. Molecular docking using shape descriptors. Journal of Computational Chemistry 1992; 13(3):380--397.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....that it is possible for the network to generate code rapidly and in a manner that can never be known apriorifor every possible condition. The inspiration for a genetic algorithm based approach to solution composition comes from nature in the form of the docking problem in molecular biology [4] [5], 6] Solutions that efficiently match a particular fault should be able to dock with the fault. Prediction for successful docking in biology can be attempted by searching for minimal energy or minimal geometric construction combinations. Here we consider a genetic algorithm used to generate a ....

B. Shoichet, D. Bodian, and I. Kuntz, "Molecular docking using shape descriptors," Journal of Comp. Chemistry, 1992.

....favourable sites for certain functional groups [50, 96] When the ligand molecule is placed in the grid region, the interaction energy can be efficiently calculated using precomputed data. Other docking approaches use only the geometry of the receptor and the ligand to define matching points. DOCK [76, 113], one of the earliest methods for docking, generates spheres inside the binding site in a way that they touch the surface of the pocket in two points and have their centers along the surface normal at one of these points. The centers of these typically overlapping spheres are the receptors ....

....in a similar way inside the ligand and their centers are the matching points of the ligand. The description of the binding pocket by the spheres described above is not unique and may seem arbitrary, but several successful predictions have been reported when matching ligand and receptor points [113]. This method has recently been extended to consider multiple conformations of the receptor, where these are available [72] As noted above, after essential points have been identified in the pocket and the ligand, the docking problem reduces to a matching problem. All possible combinations of ....

B. Shoichet, D. Bodian, and I. Kuntz. Molecular docking using shape descriptors. Journal of Computational Chemistry, 13 (3) :380-397, 1992. 34

....resource broker (see Figure 2) A layered architecture and the software stack essential for performing molecular modeling on distributed resources is depicted in Figure 3. The Grid technologies, tools, and application software used are discussed below: The DOCK software for Molecular Modeling [14]. The Nimrod Parameter Modeling Tools [3] 16] for enabling DOCK as parameter sweep application. The Nimrod G Grid Resource Broker [4] 5] for scheduling DOCK jobs on the Grid. Chemical Database (CDB) Management and Intelligent Access Tools: o CDB database Lookup Index Table Generation. o ....

....Figure 4. The receptor coordinates at the top represent 3D structure of protein. The molecular modeller identifies the active site, and other sites of interest, and uses the program sphgen to generate the sphere centers, which fill the site [13] The program grid generates the scoring grids [14]. The program dock matches spheres (generated by sphgen) with ligand atoms and uses scoring grids (from grid) to evaluate ligand orientations [13] 14] It also minimizes energy based scores [15] 6] The focus of our work is on docking molecules in CDB with receptor to identify potential ....

[Article contains additional citation context not shown here]

B. Shoichet, D. Bodian, and I. Kuntz, Molecular docking using shape descriptors, Journal of Compational Chemistry, 13(3): 380-397, 1992.

....using the Nimrod G resource broker (see Figure 2) A layered architecture and the software stack essential for performing molecular modeling on distributed resources is depicted in Figure 3. The components of Virtual Laboratory software stack are: The DOCK software for Molecular Modeling [15]. The Nimrod Parameter Modeling Tools [3] 17] for enabling DOCK as a parameter sweep application. The Nimrod G Grid Resource Broker [4] 5] for scheduling DOCK jobs on the Grid. Chemical Database (CDB) Management and Intelligent Access Tools: o CDB database Lookup Index Table Generation. ....

....coordinates at the top represent the three dimensional (3D) structure of a protein. The molecular modeller identifies the active site, and other sites of interest, and uses the program sphgen to generate the sphere centers, which fill the site [14] The program grid generates the scoring grids [15]. The program dock matches spheres (generated by sphgen) with ligand atoms and uses scoring grids (from grid) to evaluate ligand orientations [14] 15] It also minimizes energy based scores [16] 6] The focus of our work is on docking molecules in CDB with receptor to identify potential ....

[Article contains additional citation context not shown here]

B. Shoichet, D. Bodian, and I. Kuntz, Molecular docking using shape descriptors, Journal of Compational Chemistry, 13(3): 380-397, 1992.

....resource broker (see Figure 2) A layered architecture and the software stack essential for performing molecular modeling on distributed resources is depicted in Figure 3. The Grid technologies, tools, and application software used are discussed below: The DOCK software for Molecular Modeling [14]. The Nimrod Parameter Modeling Tools [3] 16] for enabling DOCK as parameter sweep application. The Nimrod G Grid Resource Broker [4] 5] for scheduling DOCK jobs on the Grid. Chemical Database (CDB) Management and Intelligent Access Tools: o CDB database Lookup Index Table Generation. o ....

....Figure 4. The receptor coordinates at the top represent 3D structure of protein. The molecular modeller identifies the active site, and other sites of interest, and uses the program sphgen to generate the sphere centers, which fill the site [13] The program grid generates the scoring grids [14]. The program dock matches spheres (generated by sphgen) with ligand atoms and uses scoring grids (from grid) to evaluate ligand orientations [13] 14] It also minimizes energy based scores [15] 6] The focus of our work is on docking molecules in CDB with receptor to identify potential ....

[Article contains additional citation context not shown here]

B. Shoichet, D. Bodian, and I. Kuntz, Molecular docking using shape descriptors, Journal of Comp. Chemistry, 13(3): 380-397, 1992.

....to a query point can be reported quickly. This is one of the most widely studied problems not only in computational geometry but in several areas of computer science, including pattern recognition [53, 64] data compression [23, 155] information retrieval [75, 162] CAD [146] molecular biology [173], image analysis [121, 123] data mining [74, 94] machine learning [52] and geographic information systems [161, 174] Most applications use so called feature vectors to map a complex object to a point in high dimensions. Examples of feature vectors include color histograms, shape descriptors, ....

B. K. Shoichet, D. L. Bodian, and I. D. Kuntz, Molecular docking using shape descriptors, J. Computational Chemistry, 13 (1992), 380-397.

....the correct solution among the high scoring ones. Ours, is a simplified scoring function which is based on geometric attributes for discarding bad steric contacts (van der Waals overlaps) and considering good ones. Variations of this scoring technique have been employed by many workers (e.g. [37, 63, 38]) all trying to tackle the problem of scoring validity and robustness (see ref. 64] for comparisons of scoring techniques) Hence, the problem of determining the optimal scoring function that will be rigorous, accurate and valid on the one hand and computationally efficient and robust on the ....

B.K. Shoichet, D.L. Bodian, and I.D. Kuntz. Molecular docking using shape descriptors. J. Comp. Chem., 13:380--397, 1992.

....to a query point can be reported quickly. This is one of the most widely studied problems not only in computational geometry but in several areas of computer science, including pattern recognition [57, 68] data compression [24, 164] information retrieval [79, 171] CAD [152] molecular biology [183], image analysis [127, 129] data mining [78, 99] machine learning [56] and geographic information systems [170, 184] Most applications use so called feature vectors to map a complex object to a point in high dimensions. Examples of feature vectors include color histograms, shape descriptors, ....

B. K. Shoichet, D. L. Bodian, and I. D. Kuntz, Molecular docking using shape descriptors, J. Computational Chemistry, 13 (1992), 380--397.

....to a query point can be reported quickly. This is one of the most widely studied problems in computational geometry because it arises in so many different areas, including pattern recognition [98, 107] data compression [25, 243] information retrieval [124, 249] CAD [213] molecular biology [261], image analysis [186, 188] data mining [123, 160] machine learning [97] and geographic information systems [246, 266] Most applications use so called feature vectors to map a complex object to a point in high dimensions. Examples of feature vectors include color histograms, shape descriptors, ....

B. K. Shoichet, D. L. Bodian, and I. D. Kuntz, Molecular docking using shape descriptors, J. Computational Chemistry, 13 (1992), 380--397.

....conformations to serial manipulator inverse kinematics. that various structural requirements on molecules can be modeled as macroscopic geometric or kinematic constraints. One example is the docking problem which examines the ways in which a ligand molecule attaches to a receptor site, see e.g. SBK92] If the docking match involves six pairs of atoms, then computing the ligand pose from the preferred bond distances is identical to the forward kinematics of the Stewart platform (see sect. 5.3) This section examines the problem of computing all conformations of a cyclic molecule, which reduces ....

B.K. Shoichet, D.L. Bodian, and I.K. Kuntz. Molecular Docking Using Shape Descriptors. J. Computational Chem., 13(3):380--397, 1992.

....favorable sites for certain functional groups [30, 59] When the ligand molecule is placed in the grid region, the interaction energy can be efficiently calculated using precomputed data. Other docking approaches use only the geometry of the receptor and the ligand to define matching points. DOCK [43, 67], one of the earliest methods for docking, generates spheres inside the binding site in a way that they touch the surface of the pocket in two points and have their centers along the surface normal at one of these points. The centers of these typically overlapping spheres are the receptor s ....

....matching points. Spheres are created in a similar way inside the ligand and their centers are the matching points of the ligand. The description of the binding pocket by the spheres described above is not unique and may seem arbitrary, but several successful predictions have been reported [67]. After essential points have been identified in the pocket and the ligand, the docking problem reduces to a matching problem. All possible combinations of ligand receptor points can be tried if their number is small [45] Simple heuristics can be used to narrow the search. DOCK, for example, ....

B. Shoichet, D. Bodian, and I. Kuntz. Molecular docking using shape descriptors. J. of Computational Chemistry, 13(3):380--397, 1992.

....GATI an animation server. We also show how these interoperable tookits, can be used in the design of custom artificial implants[12] the optimization of the connection between a jet engine and an airplane wing[11] and the efficient computation of molecular docking strategies for drug screening[10]. 2 SHASTRA : An Overview The SHASTRA environment [1] consists of a growing group of interacting applications. Some applications are responsible for managing the collaborative environment (the Kernel applications) whereas others provide specific services (the Service Applications) while yet ....

....structure approximated by Weighted Alpha Shapes[9] See Figure 7. 2. the potential energy surfaces approximated by piecewise algebraic surface interpolants [2] An interactive application is being developed in RASAYAN to compute and visualize the docking of drug and protein molecules [10] under molecular Brownian motion. The application reads in a description of the atom locations of a molecule from a file, computes the bonding information and then displays the molecule through SHASTRA s visualization toolkits. Both the computation and visualization of the potential energy ....

B. Shoichet, D. Bodian, and I. Kuntz. Molecular Docking using Shape Descriptors. The Journal of Computational Chemistry, 13(3):380--397, 1992.

.... search time compared to nearest neighbor search in the X tree (up to a factor of 4) 1 Introduction An important research issue in the field of multimedia databases is the content based retrieval of similar multimedia objects such as images, text and videos [Alt 90] Fal 94] Jag 91] MG 93] SBK 92] SH 94] However, in contrast to searching data in a relational database, a content based retrieval requires the search of similar objects as a basic functionality of the database system. Most of the approaches addressing similarity search use a so called feature transformation which transforms ....

Shoichet B. K., Bodian D. L., Kuntz I. D.: `Molecular Docking Using Shape Descriptors', Journal of Computational Chemistry, Vol. 13, No. 3, 1992, pp. 380-397.

....of user centered perspective, synchronization of frames across the walls, and tracking and wand I O. 3 Molecular Docking Formulation Computational methods for the evaluation of protein ligand and protein protein interactions have received substantial attention in recent years (see, for instance, [9, 11, 16, 17, 18, 21] and references cited therein) This attention is prompted both by the fundamental and applied significance of these interactions, and by the improvements in computational resources that have made such methods feasible. As described by Kuntz and coworkers [16, 17, 18, 19] docking methods can be ....

....(see, for instance, 9, 11, 16, 17, 18, 21] and references cited therein) This attention is prompted both by the fundamental and applied significance of these interactions, and by the improvements in computational resources that have made such methods feasible. As described by Kuntz and coworkers [16, 17, 18, 19], docking methods can be characterized by three different strategies by which the interacting molecules are juxtapositioned. First, the ligand may be positioned manually, guided by some experimental data that provides clues to the identity of the interacting surface and to the complex evaluated by ....

B. Shoichet, D. Bodian, and I. Kuntz. Molecular docking using shape descriptors. J. Comp. Chem., 13:380--397, 1992.

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Shoichet B, Bodian D, Kuntz I. Molecular docking using shape descriptors. Journal of Computational Chemistry 1992; 13(3):380--397.

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B. Shoichet, D. Bodian, and I. Kuntz, Molecular docking using shape descriptors, Journal of Compational Chemistry, 13(3), 1992.

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B. Shoichet, D. Bodian, and I. Kuntz. Molecular Docking Using Shape Descriptors. Journal of Computational Chemistry, 13(3):380--397, 1992.

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