𝔖 Bobbio Scriptorium
✦   LIBER   ✦

A Conformational Analysis Method for Understanding the Energy Landscapes of Clusters

✍ Scribed by Longjiu Cheng; Wensheng Cai ; Xueguang Shao

Publisher
John Wiley and Sons
Year
2007
Tongue
English
Weight
437 KB
Volume
8
Category
Article
ISSN
1439-4235

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

A newly developed unbiased structural optimization method, named dynamic lattice searching (DLS), is proposed as an approach for conformational analysis of atomic/molecular clusters and used in understanding the energy landscape of large clusters. The structures of clusters are described in terms of the number of basic tetrahedron (BT) units they contain. We found that the hit numbers of different structural motifs in DLS runs is proportional to the number of BTs. A parameter T~max~ is defined to limit the maximal number of atoms moved in a structural transition. Results show that T~max~ is a key parameter for modulating the efficiency of the DLS method and has a great influence on the hit number of different motifs in DLS runs. Finally, the effect of potential range on the conformational distribution of the (Morse)~98~ cluster is also discussed with different potential‐range parameters.

📜 SIMILAR VOLUMES

Evolution of physics-based methodology f
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
✍ Harold A. Scheraga; Jaroslaw Pillardy; Adam Liwo; Jooyoung Lee; Cezary Czaplewsk 📂 Article 📅 2001 🏛 John Wiley and Sons 🌐 English ⚖ 111 KB

## Abstract The evolution of our physics‐based computational methods for determining protein conformation without the introduction of secondary‐structure predictions, homology modeling, threading, or fragment coupling is described. Initial use of a hard‐sphere potential captured much of the structu

Energy landscapes of nucleophilic substi
Energy landscapes of nucleophilic substitution reactions: A comparison of density functional theory and coupled cluster methods
✍ Marcel Swart; Miquel Solà; F. Matthias Bickelhaupt 📂 Article 📅 2007 🏛 John Wiley and Sons 🌐 English ⚖ 215 KB 👁 1 views

## Abstract We have carried out a detailed evaluation of the performance of all classes of density functional theory (DFT) for describing the potential energy surface (PES) of a wide range of nucleophilic substitution (S~N~2) reactions involving, amongst others, nucleophilic attack at carbon, nitro

Monte Carlo study of ligand–protein bind
Monte Carlo study of ligand–protein binding energy landscapes with the weighted histogram analysis method
✍ Djamal Bouzida; Paul A. Rejto; Gennady M. Verkhivker 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 235 KB 👁 2 views

The thermodynamics of molecular recognition is investigated by a statistical energy landscape approach, where the temperature profile of the ligand᎐protein binding process is determined using the weighted histogram analysis method. The analysis reveals differences in the binding energy landscapes of

A hierarchical method for generating low
A hierarchical method for generating low-energy conformers of a protein-ligand complex
✍ James A. Given; Michael K. Gilson 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 304 KB 👁 2 views

A novel dynamical protocol for finding the low-energy conformations of a protein-ligand complex is described. The energy functions examined consist of an empirical force field with four different dielectric screening models; the generalized Born/surface area model also is examined. Application of th