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Strategies for the determination of pharmacophoric 3d database queries

JOURNAL OF COMPUTER-AIdEd MOLECULAR dESIGN 1997年第1期11卷 39-52页

作者： Vandrie, JH Pharmacia & Upjohn Inc. Kalamazoo MI 49001 U.S.A.

Strategies are described for constructing pharmacophoric 3d database queries, based on a series of active and inactive analogs. The results are highly selective database queries, which are consistent with the generally accepted pharmacophore for a number of systems. The foundation of these strategies is the method of Mayer, Naylor, Motoc and Marshall [J. Comput.-Aided Mol. design, 1 (1987) 3] for inferring a unique binding geometry for angiotensin-converting enzyme (ACE) inhibitors. The strategies described here generalize their approach to cases where the chemical features responsible for binding are not a priori apparent, and to cases where the binding geometry deduced by that method is not unique. The key new insight, the selectivity principle, is to rank the multiple solutions produced by the method of Mayer et al. by their selectivity, a value that is related to the proportion of a database that is returned as a database hit list. Retrospective analyses are described for d-2-antagonists, ACE inhibitors, fibrinogen antagonists, and beta(2)-antagonists.

关键词： 3d database pharmacophore database query selectivity principle d-2-antagonist pharmacophore ACE pharmacophore RGd pharmacophore beta(2)-antagonist pharmacophore

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FACE-R-A 3d database of 400 Living Individuals' Full Head CT- and Face Scans and Preliminary GMM Analysis for Craniofacial Reconstruction

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JOURNAL OF FORENSIC SCIENCES 2013年第6期58卷 1420-1428页

作者： Kustar, Agnes Forro, Laszlo Kalina, Ildiko Fazekas, Ferenc Honti, Szabolcs Makra, Szabolcs Friess, Martin Hungarian Nat Hist Museum Dept Anthropol H-1083 Budapest Hungary Idealo Internet GmbH D-10119 Berlin Germany Semmelweis Univ Dept Diagnost Radiol & Oncotherapy H-1083 Budapest Hungary TONDO SP1 Kft H-1036 Miskolc Hungary Hermann Otto Museum H-3529 Miskolc Hungary Museum Natl Hist Nat CNRS Dept Hommes UMR7206 F-75231 Paris 05 France

In the past, improvements in craniofacial reconstructions (CFR) methodology languished due to the lack of adequate 3d databases that were sufficiently large and appropriate for 3-dimensional shape statistics. In our study, we created the FACE-R database from CT records and 3d surface scans of 400 clinical patients from Hungary, providing a significantly larger sample that was available before. The uniqueness of our database is linking of two data types that makes possible to investigate the bone and skin surface of the same individual, in upright position, thus eliminating many of the gravitational effects on the face during CT scanning. We performed a preliminary geometric morphometric (GMM) study using 3d data that produces a general idea of skull and face shape correlations. The vertical position of the tip of the (soft) nose for a skull and landmarks such as rhinion need to be taken into account. Likewise, the anterior nasal spine appears to exert some influence in this regard.

关键词： forensic science forensic craniofacial reconstruction 3d database computer tomography surface scanning soft- and hard tissue covariation geometric morphometrics

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A ToF 3d database for Hand Gesture Recognition

A ToF 3D Database for Hand Gesture Recognition

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10th International Symposium on Electronics and Telecommunications (ISETC)

作者： Simion, Georgiana Caleanu, Catalin-daniel POLITEHN Univ Timisoara Fac Elect & Telecommun Timisoara Romania

ISBN: (纸本)9781467311762

Although 3d information presents, in the context of hand gesture recognition (and not only), multiple advantages in comparison with the 2d counterpart, up-to-date there are very few 3d hand gesture databases. Recently, the Time-of-Flight (ToF) principle - employed in certain range imaging 3d cameras - became more and more attractive. According to it, the measurement distance is derived from the propagation time of the light pulse between the camera and the subject for each point of the image. In this paper, we describe the development of UPT ToF 3d Hand Gesture database (UPT-ToF3d-HGdB). It represents, according to the best of our knowledge, the single database of this type which is publicly available.

关键词： Hand gesture recognition Time-of-Flight 3d database

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Chemical function based pharmacophore models as suitable filters for virtual 3d-database screening

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JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 2000年第1-2期503卷 59-72页

作者： Langer, T Hoffmann, Rd Bachmair, F Begle, S Univ Innsbruck Inst Pharmaceut Chem A-6020 Innsbruck Austria Parc Club Orsay Univ Mol Simulat SARL F-91838 Orsay France

In this paper a description of the concept of chemical function based pharmacophore models is given. Their generation based on the knowledge of a set of active ligands for a biological target is discussed as well as the utility of the models obtained to retrieve new potentially bio-active compounds from large 3d databases. This concept is exemplified describing the application to two different biological targets: the retinoic receptor family and the enzyme aldose reductase. (C) 2000 Elsevier Science B.V. All rights reserved.

关键词： chemical feature based pharmacophores virtual screening 3d database

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3d Face database for human pattern recognition

3D Face database for human pattern recognition

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7th International Symposium on Instrumentation and Control Technology

作者： Song, LiMei Lu, Lu SW Univ Sci & Technol Informat Engn Coll Mianyang 621010 Sichuan Peoples R China

ISBN: (纸本)9780819473615

Face recognition is an essential work to ensure human safety. It is also an important task in biomedical engineering. 2d image is not enough for precision face recognition. 3d face data includes more exact information, such as the precision size of eyes, mouth, etc. 3d face database is an important part in human pattern recognition. There is a lot of method to get 3d data, such as 3d laser scan system, 3d phase measurement, shape from shading, shape from motion, etc. This paper will introduce a non-orbit, non-contact, non-laser 3d measurement system. The main idea is from shape from stereo technique. Two cameras are used in different angle. A sequence of light will project on the face. Human face, human head, human tooth, human body can all be measured by the system. The visualization data of each person can form to a large 3d face database, which can be used in human recognition. The 3d data can provide a vivid copy of a face, so the recognition exactness can be reached to 100%. Although the 3d data is larger than 2d image, it can be used in the occasion where only few people include, such as the recognition of a family, a small company, etc.

关键词： Pattern recognition shape from stereo 3d visualization 3d database

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database structure and searching in MACCS-3d

Tetrahedron Computer Methodology

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Tetrahedron Computer Methodology 1990年第6 PART C期3卷 653-664页

作者： Christie, Bradley d. Henry, douglas R. Wipke, W.Todd Moock, Thomas E. Molecular Design Limited San Leandro CA 94577 2132 Farallon Dr United States

The MACCS-3d program was developed to provide a three-dimensional (3d) structural database system for structure, substructure, geometric, and data searching purposes. Applications of the program include discovery of new drugs and agrochemicals to fit known or postulated pharmacophores, and identification of polymers and commercial chemicals whose physical and chemical properties depend on 3d structural features. This paper presents details of the data structures and algorithms used for 3d structural representation, storage, and searching in MACCS-3d. These include algorithms for exact match, substructure, geometric, submodel, and combined 3d structure-data searching. We also describe mechanisms used for 3d data storage and geometric search keys. Integration of MACCS-3d with new chemical representation and search capabilities of the MACCS-II system are briefly described. Finally, new developments in MACCS-3d are described, in light of current and future trends in 3d searching. © 1992.

关键词： 3d database 3d searching Chemical information management

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A GENETIC ALGORITHM FOR THE AUTOMATEd GENERATION OF MOLECULES WITHIN CONSTRAINTS

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JOURNAL OF COMPUTER-AIdEd MOLECULAR dESIGN 1995年第2期9卷 181-202页

作者： GLEN, RC PAYNE, AWR WELLCOME RES LABS DIV INFORMAT SERVBECKENHAM BR3 3BSKENTENGLAND

A genetic algorithm has been designed which generates molecular structures within constraints. The constraints may be any useful function, for example an enzyme active site, a pharmacophore or molecular properties from pattern recognition or rule-induction analyses. The starting point may be random or may utilise known molecules. These are modified to 'grow' into families of structures which, using the evolutionary operators of selection, crossover and mutation evolve to better tit the constraints. The basis of the algorithm is described together with some applications in lead generation, 3d database construction and drug design. Genetic algorithms of this type may have wider applications in chemistry, for example in the design and optimisation of new polymers, materials (e.g. superconducting materials) or synthetic enzymes.

关键词： dE NOVO dRUG dESIGN EVOLUTION AUTOMATEd STRUCTURE GENERATION 3d database EXPERT SYSTEM

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Robust Estimation of driver Posture in the Presence of Lighting Changes

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ELECTRONICS ANd COMMUNICATIONS IN JAPAN 2009年第2期92卷 10-20页

作者： Takahashi, daisuke Okamoto, Noriyoshi Okamoto Laboratory Kanto Gakuin University Japan

In this study, we aim for posture estimation that considers the influence of lighting changes. We propose an algorithm that considers a bad condition by using 3d data and 2d animation. The decrease of the gaze forward rate caused by the psychological condition and ensuing tiredness is a problem of safety driving. There is a technique for detecting looking away and looking down for a long time by estimation of the driver's face posture from the image as this method of settlement. However, the conventional technique uses images in the posture estimation, which has the problem of a strong influence on the lighting condition and the size of the database. This technique pays too much attention to lighting changes 3d data and texture information. Making the database solved these problems;the accuracy average obtained was 89% and the estimation speed was 6 f/s. (C) 2009 Wiley Periodicals, Inc. Electron Comm Jpn, 92(2): 10-20, 2009;Published online in Wiley Inter-Science (***). dOI 10.1002/ecj.10012

关键词： texture driving posture lighting changes 3d database

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Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors

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JOURNAL OF COMPUTER-AIdEd MOLECULAR dESIGN 2000年第5期14卷 411-425页

作者： Fox, T Haaksma, EEJ Boehringer Ingelheim KG Dept Chem Res Struct Res D-88397 Biberach Germany

We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRId. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3d database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.

关键词： active site mapping flexible query GRId structure based screening 3d database thrombin

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Relibase:: design and development of a database for comprehensive analysis of protein-ligand interactions

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JOURNAL OF MOLECULAR BIOLOGY 2003年第2期326卷 607-620页

作者： Hendlich, M Bergner, A Günther, J Klebe, G Univ Marburg Inst Pharmaceut Chem D-35032 Marburg Germany Lion Biosci ChemInformat D-69123 Heidelberg Germany Cambridge Crystallog Data Ctr Cambridge CB2 1EZ England

Knowledge discovery from the exponentially growing body of structurally characterised protein-ligand complexes as a source of information in structure-based drug design is a major challenge in contemporary drug research. Given the need for powerful data retrieval, integration and analysis tools, Relibase was developed as a database system particularly designed to handle protein-ligand related problems and tasks. Here, we describe the design and functionality of the Relibase core database system. Features of Relibase include, e.g. the detailed analysis of superimposed ligand binding sites, ligand similarity and substructure searches, and 3d searches for protein-ligand and protein-protein interaction patterns. The broad range of functions provided in Relibase and its high level of data integration, along with its flexible and intuitive interface, makes Relibase an invaluable data mining tool which can significantly enhance the drug development process. An example, illustrating a 3d query for quarternary ligand nitrogen atoms interacting with aromatic ring systems in proteins, a pattern found in pharmaceutically relevant target proteins such as, e.g. acetylcholine-esterase, is discussed. (C) 2003 Elsevier Science Ltd. All rights reserved.

关键词： structure-based drug design protein-ligand interaction 3d database data mining

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