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Protein-Ligand Docking Based on ß-shape
2009 Edition, June 1, 2009 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

Protein-ligand docking is to predict a ligand conformation and orientation with respect to a protein within its binding site, and has been known to be essential for the development of new drugs. The protein-ligand docking problem is usually...

Side-chain flexibility in protein docking
2015 Edition, August 1, 2015 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

Conventional protein docking methods use rigid docking algorithms but the results have been unsatisfactory, because protein structures are flexible in live environments. In this study, the side-chain flexibility is introduced into protein docking. First,...

An isometry-invariant spectral approach for protein-protein docking
2013 Edition, November 1, 2013 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

The protein docking problem refers to the task of predicting the appropriate matching of one protein molecule (the receptor) to another (the ligand), when attempting to bind them to form a stable complex. Research shows that matching the three-dimensional geometric...

An efficient searching algorithm based on local shape complementarity of hydrogen bonds and relaxation labeling for protein-ligand docking
2013 Edition, Volume 02, July 1, 2013 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

A new search algorithm based on the hydrogen bond shape complementarity and relaxation labeling for fast protein-ligand docking is proposed. Given that the protein-ligand binding sites are demonstrated to relate with the cavities in the...

SP-Dock: Protein-Protein Docking Using Shape and Physicochemical Complementarity
2013 Edition, Volume 10, January 1, 2013 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

In this paper, a framework for protein-protein docking is proposed, which exploits both shape and physicochemical complementarity to generate improved docking predictions. Shape complementarity is achieved by matching local surface patches. However, unlike...

Visual Analysis with Dynamic Geometric Complementarity and Physicochemical Matching in Protein Docking
2014 Edition, July 1, 2014 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

Prediction of the 3D structure of protein-protein complexes is crucial for understanding the biological system of life and thus for designing drugs. However it is a challenging problem due to the flexibility of the backbone and side-chains of the receptor and ligand. In this...

3D protein-protein docking using shape complementarity and fast alignment
2011 Edition, September 1, 2011 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

In this paper, a novel approach for fast protein-protein docking based on geometric complementarity is introduced. Complementarity matching is achieved using a rotation-invariant 3D shape descriptor, the Shape Impact Descriptor (SID). Rotation...

Docking of protein molecules
1994 Edition, Volume 2, January 1, 1994 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

The problem of receptor-ligand recognition and binding is encountered in a very large number of biological processes, The behavior of the molecules depends both on their geometric shape and on the chemical interactions among their atoms. This work addresses only the...

Energy-field reconstruction for haptic-based molecular docking using energy minimization processes
2007 Edition, October 1, 2007 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

This paper presents a new method allowing haptic feedback in molecular docking simulations using a minimization process. These simulations, classically used by the pharmaceutical industry, for example Sanofl-Aventis, are based on the energy description of atoms to estimate the...

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