Molecular Access Systems

Figure 9.3. MACCS— the Molecular ACCess System—an early structure indexing system. This program originally used fixed menus for searching, registration, and reporting. Later versions allowed users to customize the menus. The figure shows the result of a 3D pharmacophore search for ACE inhibitors. Out of a database of 115,000 structures, 21 fit the 2D and 3D requirements of the search query. The user could typically browse the "hits" from the search, save the list of structures to a list file, and output the structures to a structure-data file (SDFile). The MACCS database was a proprietary flat database system in which data of a given type, say, formula, was stored in a given file, indexed by the compound ID number.

Dill, J.D. Hounshell, W.D. Marson, S. Peacock, S. Wipke, W.T. Search and Retrieval Using an Automated Molecular Access System , paper presented at 182nd National Meeting of the American Chemical Society, New York, August, 1981. 

Fig. 2.12 Molecular Design Limited Molecular ACCess System (MACCS) fingerprints computed for Ames data set...

D. J. Polton, Online Rev., 6, 235 (1982). Installation and Operational Experiences with MACCS (Molecular Access System). 

MACCS (Molecular ACCess System), developed and distributed by MDL Information Systems, San Leandro, CA. This older system is being augmented with ISIS (Ref. 23). 

D similarities (see Seet. 1.2 for details). This raises the question of whether 2-D similarities perform equally or better than 3-D methods in tasks commonly carried out in chemical informatics. Conclusive results have not been achieved to date. Nevertheless, it appears that 2-D methods can in many cases perform equally well and in some cases outperform 3-D methods [17, 18] in a variety of tasks. These tasks include similarity-based searches designed to identify new, potentially active molecules based on previously determined actives and to identify molecules with potentially similar values for properties of interest in drag research such as logP— both are examples of the SPP. In addition, these workers showed that of the 2-D methods considered molecular ACCess system (MACCS) stractural-key-based fingerprints (FPs) (yide infra) consistently exhibited the best performance. 

The first chapter, on Conformational Dynamics, includes discussion of several rather recent computational approaches to treat the dominant slow modes of molecular dynamical systems. In the first paper, SCHULTEN and his group review the new field of steered molecular dynamics (SMD), in which large external forces are applied in order to be able to study unbinding of ligands and conformation changes on time scales accessible to MD... 

This decade also saw the first major developments in molecular graphics. The first multiple-access computer was built at MIT (the so-called project MAC), which was a prototype for the development of modern computing. This device included a high-performance oscilloscope on which programs could draw vectors very rapidly and a closely coupled trackball with which the user could interact with the representation on the screen. Using this equipment, Levinthal and his team developed the first molecular graphics system, and his article in Scientific American [25] remains a classic in the field and laid the foundations for many of the features that characterize modern day molecular graphics systems. 

Luminescence spectroscopy provides simple access to the splitting of the ground multiplet but this technique is not always accessible due to nonradiative decay and strong ligand absorptions as encountered, for example, in the [Ln(Pc)]-/0 systems. For these reasons, alternative spectroscopic tools should be available for magnetochemists. The use of INS as a spectroscopic probe for molecular magnetic systems has recently been reviewed by Guidi [36], Amoretti et al. [37]... 

It is evident from the properties accessible that PPys may prove to be very useful materials in the future. To date, the synthetic difficulties encountered have thwarted progress and made processible and well-characterized, high molecular weight systems largely untenable. Future breakthroughs are required in this area to overcome these obstacles. 

The theory described here was originally developed by the author, as also the specific targeted application of the theory to molecular modeling of the transition metal complexes. This and other original methods of molecular modeling described here have been implemented in FORTRAN program suits. They are a kind of research software available for use to other researchers through the Net Laboratory access system which provides sample input files and minimal reference information to start with, at http //www.qcc.ru/ netlab. 

In this chapter we have presented a multi-scale method for molecular dynamics simulations of shock compression and characterized its behaviour. This method attempts to constrain the molecular dynamics system to the sequence of thermodynamic states that occur in a shock wave. While we have presented one particular approach, it is certainly not unique and there are likely a variety of related approaches to multi-scale simulations that have a variety of differing practical properties. These methods open the door to simulations of shock propagation on the longest timescales accessible by molecular d5nnamics and the use of accurate but computationally costly material descriptions like density fimctional theory. It is our belief that this method promises to be a valuable tool for elucidation of new science in shocked condensed matter. 

MACCS (Molecidar ACCess System), 1989, developed and distributed by Molecular Design Ltd, San Leandro, Califomia, U.S.A. 

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