𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Efficient electrostatic solvation model for protein-fragment docking

✍ Scribed by Nicolas Majeux; Marco Scarsi; Amedeo Caflisch

Publisher
John Wiley and Sons
Year
2000
Tongue
English
Weight
327 KB
Volume
42
Category
Article
ISSN
0887-3585

No coin nor oath required. For personal study only.

✦ Synopsis

A method is presented for the fast evaluation of the binding energy of a protein-small molecule complex with electrostatic solvation. It makes use of a fast preprocessing step based on the assumption that the main contribution to electrostatic desolvation upon ligand binding originates from the displacement of the first shell of water molecules. For a rigid protein, the precomputation of the energy contributions on a set of grids allows the estimation of the energy in solution of about 300 protein-fragment binding modes per second on a personal computer. The docking procedure is applied to five rigid binding sites whose size ranges from 17 residues to a whole protein of 107 amino acids. Using a library of 70 mainly rigid molecules, known micromolar inhibitors or close analogs are docked and prioritized correctly. The docking based rank-ordering of the library requires about 5 h and is proposed as a complementary approach to structure-activity relationships by nuclear magnetic resonance. Proteins 2001;42:256 -268.

📜 SIMILAR VOLUMES

Use of the FACTS solvation model for pro
Use of the FACTS solvation model for protein–ligand docking calculations. Application to EADock
✍ Vincent Zoete; Aurélien Grosdidier; Michel Cuendet; Olivier Michielin 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 297 KB

## Abstract Protein–ligand docking has made important progress during the last decade and has become a powerful tool for drug development, opening the way to virtual high throughput screening and __in silico__ structure‐based ligand design. Despite the flattering picture that has been drawn, recent

Prodock: Software package for protein mo
Prodock: Software package for protein modeling and docking
✍ Trosset, Jean-Yves; Scheraga, Harold A. 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 240 KB 👁 2 views

A new software package, PRODOCK, for protein modeling and flexible docking is presented. The protein system is described in internal coordinates with an arbitrary level of flexiblity for the proteins or ligands. The protein is represented by an all-atom model with the ECEPPr3 or AMBER IV force field

Performance comparison of generalized bo
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
✍ Michael Feig; Alexey Onufriev; Michael S. Lee; Wonpil Im; David A. Case; Charles 📂 Article 📅 2003 🏛 John Wiley and Sons 🌐 English ⚖ 205 KB

## Abstract This study compares generalized Born (GB) and Poisson (PB) methods for calculating electrostatic solvation energies of proteins. A large set of GB and PB implementations from our own laboratories as well as others is applied to a series of protein structure test sets for evaluating the

CHARMM fluctuating charge force field fo
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
✍ Sandeep Patel; Alexander D. Mackerell Jr.; Charles L. Brooks III 📂 Article 📅 2004 🏛 John Wiley and Sons 🌐 English ⚖ 416 KB

## Abstract A fluctuating charge (FQ) force field is applied to molecular dynamics simulations for six small proteins in explicit polarizable solvent represented by the TIP4P‐FQ potential. The proteins include 1FSV, 1ENH, 1PGB, 1VII, 1H8K, and 1CRN, representing both helical and β‐sheet secondary s

QSAR model for alignment-free prediction
QSAR model for alignment-free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP-lattice networks
✍ Santiago Vilar; Humberto González-Díaz; Lourdes Santana; Eugenio Uriarte 📂 Article 📅 2008 🏛 John Wiley and Sons 🌐 English ⚖ 413 KB

## Abstract Network theory allows relationships to be established between numerical parameters that describe the molecular structure of genes and proteins and their biological properties. These models can be considered as quantitative structure–activity relationships (QSAR) for biopolymers. The wor