3D key

ChemX/ChemDiverse, PharmPrint, OSPPREYS, 3D Keys, Tuplets... 

The Accelrys implementation of pharmacophore fingerprint descriptors is called 3D Keys. This application is based on standard Catalyst feature definitions and is a part of the Cerius2 software package [7]. 

MACCS-3D Single/multiple conformation 2D/3D CONCORD Internal registration system 2D keys 3D keys MDL... 

Each of the automated techniques we have described has its own strengths and weaknesses. The 3D key approach provided within ChemDBS-SD o is attractive, because all stages of the process, from conformational analysis through model building, are handled automatically. The technique tends to produce many models, however. This is not necessarily a problem, but it does mean that more false positives will need to be weeded out during the validation... 

The key company of the new NDT- centre is HAPEG (Hattinger Priif- und Entwicklungs-gesellschaft), which operates a Computed Tomography system and offers service measurements on test samples of their customers [1]. The basic set up and technical details of this CT-system are presented in this paper. Details of the extension towards 3D visualisation, 3D-Tomography and the software involved are presented in a different paper [2]. 

D database searching. As each conformation is generated an appropriate bit is set in the binary key. At me, the binary key appropriate to the pharmacophore is set up and compared with the keys in the database. 

Finally, 3D pharmacophores can be used to provide a naturally partitioned space. By com bining the pharmacophore keys of a set of molecules one can determine how many of th potential 3- or 4- point pharmacophores are accessible to the set and easily identify thos which are not represented. This use of pharmacophores is the basis of a method namei Pharmacophore-Derived Queries (PDQ) [Pickett et al. 1996]. One feature of this particula method is that most molecules will occupy more than one cell (as nearly all molecules wil contain more than one 3-point pharmacophore due to the functionality present an( conformational flexibility). This contrasts with the usual situation, wherein each molecul occupies just one cell. 

This article has been focussing on poly(phenylene)s with 1,4-(pnra-)phenylene units since these polymers play a key role in the synthesis-driven search for electronic materials. From this article it has become clear that poly(phenylene) chemistry has not restricted its attention to linear (1D-) structures, but has more recently developed into 2D- and 3D-structures as well, the latter serving as functional shape-persistent nanoparticlcs. 

IP3 Receptors. Figure 2 Key structural features of IP3 receptors. The key domains are shown in the central block. The upper structures show the suppressor domain (PDB accession code, 1XZZ) and the IBC (1N4K) with its (red) and p (blue) domains. A proposed structure for the pore region is shown below, with the selectivity filter shown in red only two of the four subunits are shown. The lowest panel shows reconstructed 3D structures of IP3R1 viewed (left to right) from ER lumen, the cytosol and in cross-section across the ER membrane (reproduced with permission from [4]). 

Moreover, molecular modeling is one key method of a wide range of computer-assisted methods to analyze and predict relationships between protein sequence, 3D-molecular structure, and biological function (sequence-structure-function relationships). In molecular pharmacology these methods focus predominantly on analysis of interactions between different proteins, and between ligands (hormones, drugs) and proteins as well gaining information at the amino acid and even to atomic level. 

Thus the key experimental observation Equation (7.11), is satisfied in presence of spillover. When an external overpotential AUWR is applied, with a concomitant current, I, and O2 flux I/2F, although UWR is not fixed anymore by the Nemst equation but by the extremally applied potential, still the work function Ow will be modified and Equations (7.11) and (7.12), will remain valid as long as ion spillover is fast relative to the electrochemical charge transfer rate I/2F.21 This is the usual case in solid state electrochemistry (Figs. 7.3b, 7.3d) as experimentally observed (Figs. 5.35, 5.23, 7.4, 7.6-7.9). 

The present volume is dedicated to the measurement and the predichon of key physicochemical drug properhes with relevance for their biological behavior, including ionizahon and H-bonding, solubihty, Hpophihdty as well as 3D structure and conformahon. 

One element of database generation that is a key consideration is whether to expand the representative compounds to include alternative tautomers, protonated and deprotonated forms of the molecule, and also to enumerate stereochemistry fully if not specified in the input. Depending on the molecules in question and the options considered, these can lead to a 10-fold increase in the size of the database to be explored. However, such an expansion is necessary if methods are used that are sensitive to such chemical precision (e.g., docking). For 3D similarity searching, it is sometimes more efficient to consider various modifications to the query, leading to multiple searches against a smaller database. 

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