𝔖 Bobbio Scriptorium
✦   LIBER   ✦

A versatile method for systematic conformational searches: Application to CheY

✍ Scribed by Robert J. Petrella

Publisher
John Wiley and Sons
Year
2011
Tongue
English
Weight
538 KB
Volume
32
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

A novel molecular structure prediction method, the Z Method, is described. It provides a versatile platform for the development and use of systematic, grid‐based conformational search protocols, in which statistical information (i.e., rotamers) can also be included. The Z Method generates trial structures by applying many changes of the same type to a single starting structure, thereby sampling the conformation space in an unbiased way. The method, implemented in the CHARMM program as the Z Module, is applied here to an illustrative model problem in which rigid, systematic searches are performed in a 36‐dimensional conformational space that describes the relative positions of the 10 secondary structural elements of the protein CheY. A polar hydrogen representation with an implicit solvation term (EEF1) is used to evaluate successively larger fragments of the protein generated in a hierarchical build‐up procedure. After a final refinement stage, and a total computational time of about two‐and‐a‐half CPU days on AMD Opteron processors, the prediction is within 1.56 Å of the native structure. The errors in the predicted backbone dihedral angles are found to approximately cancel. Monte Carlo and simulated annealing trials on the same or smaller versions of the problem, using the same atomic model and energy terms, are shown to result in less accurate predictions. Although the problem solved here is a limited one, the findings illustrate the utility of systematic searches with atom‐based models for macromolecular structure prediction and the importance of unbiased sampling in structure prediction methods. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

📜 SIMILAR VOLUMES

Conformational energy calculations for d
Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate
✍ Janet M. Thornton; Peter M. Bayley 📂 Article 📅 1976 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 860 KB

## Abstract A systematic study of the conformational states of the dinucleotide diadenosine 5′,5′‐pyrophosphate (AppA), an analog of the coenzyme NAD^+^, has been made using semi‐empirical energy calculations. Taking low‐energy mononucleotide structures as starting conformations, energy minimizatio

Introduction of a Generally Applicable M
Introduction of a Generally Applicable Method to Estimate Retrieval of Active Molecules for Similarity Searching using Fingerprints
✍ Martin Vogt; Jürgen Bajorath 📂 Article 📅 2007 🏛 John Wiley and Sons 🌐 English ⚖ 409 KB 👁 1 views

## Abstract Fingerprints are bit string representations of molecular structure and properties and are among the most widely used computational tools for similarity searching and database screening. Various fingerprint designs are available and their search performance is in general strongly depende

A Chebyshev Polynomial Interval-Searchin
A Chebyshev Polynomial Interval-Searching Method ("Lanczos Economization") for Solving a Nonlinear Equation with Application to the Nonlinear Eigenvalue Problem
✍ John P. Boyd 📂 Article 📅 1995 🏛 Elsevier Science 🌐 English ⚖ 362 KB

To search a given real interval for roots, our algorithm is to replace \(f(\lambda)\) by \(f_{N}(\lambda)\), its \(N\)-term Chebyshev expansion on the search interval \(\lambda \in\left[\lambda_{\min }, \lambda_{\max }\right]\), and compute the roots of this proxy. This strategy is efficient if and