𝔖 Bobbio Scriptorium
✦   LIBER   ✦

An efficient molecular docking using conformational space annealing

✍ Scribed by Kyoungrim Lee; Cezary Czaplewski; Seung-Yeon Kim; Jooyoung Lee

Publisher
John Wiley and Sons
Year
2004
Tongue
English
Weight
159 KB
Volume
26
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

Molecular docking falls into the general category of global optimization problems because its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor–ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA, and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with the minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions, and torsional energy terms, is calculated using the AMBER94 all‐atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA, and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native‐like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 78–87, 2005

📜 SIMILAR VOLUMES

LigDockCSA: Protein–ligand docking using
LigDockCSA: Protein–ligand docking using conformational space annealing
✍ Woong-Hee Shin; Lim Heo; Juyong Lee; Junsu Ko; Chaok Seok; Jooyoung Lee 📂 Article 📅 2011 🏛 John Wiley and Sons 🌐 English ⚖ 426 KB 👁 1 views

## Abstract Protein–ligand docking techniques are one of the essential tools for structure‐based drug design. Two major components of a successful docking program are an efficient search method and an accurate scoring function. In this work, a new docking method called LigDockCSA is developed by us

Conformational studies of human islet am
Conformational studies of human islet amyloid peptide using molecular dynamics and simulated annealing methods
✍ U. Ilangovan; A. Ramamoorthy 📂 Article 📅 1998 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 287 KB 👁 1 views

Molecular dynamics simulations and simulated annealing in vacuum, model aqueous solution, and simulated membrane were used to analyze the conformational preferences of a segment spanning 20-29 residues of human islet amyloid polypeptide, [referred to as IAPP H (20-29)]. Molecular dynamics simulation

Comparative analysis of the conformation
Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics
✍ Francesc J. Corcho; Josep Canto; Juan J. Perez 📂 Article 📅 2004 🏛 John Wiley and Sons 🌐 English ⚖ 410 KB

## Abstract The present study describes an extensive conformational search of substance P using two different computational methods. On the one hand, the peptide was studied using the iterative simulated annealing, and on the other, molecular dynamics simulations at 300 and 400 K. With the former m

Efficient exploration of conformational
Efficient exploration of conformational space using the stochastic search method: application to β-peptide oligomers
✍ Jayaraman Chandrasekhar; Martin Saunders; William L. Jorgensen 📂 Article 📅 2001 🏛 John Wiley and Sons 🌐 English ⚖ 166 KB

## Abstract An efficient and general strategy for the determination of all low‐energy minima of a molecule, viz., the stochastic conformational jump procedure, has been implemented in the BOSS package. In this method, a new structure is generated by random movement (“kick”) of individual atoms with

Reducing CAS-SDCI space. Using selected
Reducing CAS-SDCI space. Using selected spaces in configuration interaction calculations in an efficient way
✍ José Pitarch-Ruiz; José Sánchez-Marín; Daniel Maynau 📂 Article 📅 2002 🏛 John Wiley and Sons 🌐 English ⚖ 115 KB

## Abstract A new method is presented, which allows an important reduction of the size of some Configuration Interaction (CI) matrices. Starting from a Complete Active Space (CAS), the numerous configurations that have a small weight in the CAS wave function are eliminated. When excited configurati