𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Fast and accurate computation schemes for evaluating vibrational entropy of proteins

✍ Scribed by Beisi Xu; Hujun Shen; Xiao Zhu; Guohui Li

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

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

Standard normal mode analysis (NMA) method is able to calculate vibrational entropy of proteins, but it is computationally intensive, especially for large proteins. To evaluate vibrational entropy efficiently and accurately, we, here, propose computation schemes based on coarse‐grained NMA methods. This can be achieved by rescaling coarse‐grained results with a specific factor that is derived on the basis of the linear correlation of protein vibrational entropy between standard NMA and coarse‐grained NMA. Our coarse‐grained NMA computation schemes can repeat correctly and efficiently the results of standard NMA for large proteins. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

📜 SIMILAR VOLUMES

Fast and accurate molecular dynamics sim
Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer
✍ Komeiji, Yuto; Uebayasi, Masami; Takata, Ryo; Shimizu, Akihiro; Itsukashi, Keiji 📂 Article 📅 1997 🏛 John Wiley and Sons 🌐 English ⚖ 428 KB 👁 3 views

a The 10-ps configuration of each trajectory was used as the initial configuration. The system was simulated for 5 ps using a ( ) microcanonical ensemble with various time steps. Then, the RMSF E and the computation time was examined. r tot b ( ) Hard forces H : bond, angle, and torsion. c ( ) Mediu

New and fast statistical-thermodynamic m
New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy
✍ A. M. Ruvinsky; A. V. Kozintsev 📂 Article 📅 2005 🏛 John Wiley and Sons 🌐 English ⚖ 101 KB 👁 1 views

## Abstract We present a novel method to estimate the contributions of translational and rotational entropy to protein‐ligand binding affinity. The method is based on estimates of the configurational integral through the sizes of clusters obtained from multiple docking positions. Cluster sizes are

Computer simulation for the evaluation o
Computer simulation for the evaluation of static and dynamic priority schemes in an ATM multiplexer with multimedia traffic
✍ Saud Al-Barrak; Adnan Nouh; Saad Haj Bakry 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 230 KB 👁 2 views

This paper is concerned with the evaluation of static and dynamic priority schemes for ATM multiplexers using digital computer simulation and has three main parts. The first provides a basic computer simulation model of an ATM multiplexer with multimedia traffic streams that enables investigation of