Conformer generator

Many approaches and methods for the generation of multiple conformations have been developed and published since the early 1980s. Below we describe briefly some of the basic concepts and methods of automatic conformer generation. However, interested readers are referred to Chapter 11, Section 7.2 in the Handbook, where the approaches to automatic generation of ensembles of conformations and the program systems that have been developed are described in detail. 

The functionality available in MedChem Explorer is broken down into a list of available computational experiments, including activity prediction, align/ pharmacophore, overlay molecules, conformer generation, property calculation, and database access. Within each experiment, the Web system walks the user through a series of questions that must be answered sequentially. The task is then submitted to a remote server, where it is performed. The user can view the progress of the work in their Web browser at any time. Once complete, the results of the calculation are stored on the server. The user can then run subsequent experiments starting with those results. The Web interface includes links to help pages at every step of the process. 

Conformer generation is used to obtain a list of likely confonners of the molecule. This list can include a set number of the lowest-energy confonners or a number of confonners that give the most diversity of possible shapes. 

CONCORD 2-D to 3-D converters converter/conformation generator Tripos... 

WIZARD converter/conformation generator Dolata Leach... 

Let A = yc, , 1 < / < Nc, be conformations generated for C using a computational method. Because the global free energy minimum conformation is expected to statistically dominate the thermodynamic ensemble, the predicted binding activity for C is determined by (C)=min F y. ) = F(yf ). 

Tab. 1.2 Limits, ranges and mean values 99.9% confidence limits of the molecular properties of acetylcholine conformers generated during MD simulations.

The missing link between the constitution of a molecule and its 3D structure in computahonal chemistry is a technique capable of automatically generating 3D models starhng from the connectivity information of a given molecule. Due to its basic role, 3D structure generation is one of the fundamental problems in computahonal chemistry. As a consequence, in recent years a number of automahc 3D model builders and conformer generators have become available. For two comprehensive reviews, see Refs. [3, 4]. 

To illustrate the number of conformers generated for a typical pharmaceutical like database, OMEGA calculations were carried out for the 450000 compounds... 

Fig. 8.7 The average number of conformations generated as a function of the number of rotatable bonds for compounds in the GVK Bio database.

Sadowski, J., Bostrom, J. MIMUMBA revisited torsion angle rules for conformer generation derived from X-ray structures. /. Chm. Inf. Model. 2006, 46, 2305-2309. 

Fig. 1. A scheme of conformational generation of polypeptides, copolypeptides and proteins.

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