NDLI: In Silico Drug Screening Based on a Protein-Compound Affinity Matrix

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2008 International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies

Table of contents

Preface

Committees

In-bed Patients Behaviour Monitoring System

A Data Fusion Approach in Protein Homology Detection

Identifying Disease Susceptible DNA Regions Using Underlying Odds Ratio Contour Analysis

Fister-Panetta Upper Bound for Cancer Growth. Some Computational Remarks

Failure Prediction Mechanisms in Cluster Systems

Directional Invariance of Co-occurrence Matrices within the Liver

"Blast Those Sequences': A Gridified Framework for Bioinformatics Blast Using the A3pviGrid

A New Modeling for Finding Optimal Weighted Distances

Effects of Improper Spectral Delay on Speech Recognition with Cochlear Implants: A Simulation Study

In Silico Drug Screening Based on a Protein-Compound Affinity Matrix

TVscreen: Trend Vector Virtual SCREENing of Large Commercial Compounds Collections

MMsINC®: A New Public Large-Scale Chemoinformatics Database System

Concept of Associated Photodynamic Therapy with Porphyrin Cis-Platin Drug System and Applications on HeLa Cells

New Chessboard (8×8) Representation of the Standard Genetic Code, and Its Application for Representing Primary Structures of Proteins

Combining Boundaries and Ratings from Multiple Observers for Predicting Lung Nodule Characteristics

Network P2P for Exploring and Visualization of Proteomic Data: Possibility of Handling Data and Analysing Them under Different Perspectives

sBGMM: A Stratified Beta-Gaussian Mixture Model for Clustering Genes with Multiple Data Sources

Mathematical Description of Biological Structures and Mechanisms

Microdevice for Isolating Viable Circulating Tumor Cells

Biosensing Based on Surface Plasmon Resonance of Gold Nanohole and Nanoring Arrays Fabricated by a Novel Nanosphere Lithography Technique

Particle Transfer and Detection in a Microspheres Based Detoxification System

UUTE Home Network for Wireless Health Monitoring

RN-Cluster: Discovering Coherent Biclusters Which is Robust to Noise

Design of Microarray Probes for Detection of Mutations

Next-Generation Collaboration Environments for Interactive Tele-medical Consultation

Towards Better Outliers Detection for Gene Expression Datasets

Exploiting Codon-Triplets Association for Genome Primary Structure Analysis

Studying the Evolution of Codon Context in Conserved Gene Sequences

Grouping Levels of Exposure with Same Observable Effects before Class Prediction in Toxicogenomics

A Microarray Information Database

Analyzing Multivariate Calibration Techniques for Glucose Level Prediction in Non-invasive Human Tongue Spectra

Author index

In Silico Drug Screening Based on a Protein-Compound Affinity Matrix

Content Provider	IEEE Xplore Digital Library
Author	Fukunishi, Y.
Copyright Year	2008
Description	Author affiliation: Biomedicinal Inf. Res. Center, Nat. Inst. of Adv. Ind. Sci. & Technol., Tokyo (Fukunishi, Y.)
Abstract	We developed a new method to improve the accuracy of molecular interaction data using a protein-compound affinity matrix calculated by protein-compound docking software. We approximated the protein-compound binding free energy as a linear combination of the raw docking scores of the compound with many different proteins. The coefficients of the linear combination were estimated based on the amino-acid sequence similarities among proteins. This method was applied to in silico screening of the active compounds of five target proteins using multiple target screening, and it increased the hit ratio by several times compared to that given by the raw docking scores. The hit ratio also becomes robust against the difference of target proteins. In addition, we have developed some methods based on a protein-compound affinity matrix. When some active compounds were known, a consensus score, which combines the structure-based and ligand-based screening results, was applied to a target. Finally, we could achieve a high hit ratio for some targets by using a combination of screening methods.
Starting Page	53
Ending Page	58
File Size	502635
Page Count	6
File Format	PDF
ISBN	9780769531915
DOI	10.1109/BIOTECHNO.2008.10
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-06-29
Publisher Place	Romania
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Drugs Protein engineering Solvents Pharmaceutical technology Statistical analysis Fingerprint recognition Multiple target screening method Machine-learning score modification Physics Databases Docking score index method Robustness Direct score modification Bioinformatics Affinity fingerprint
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Bioinformatics Based Ligand-Docking and in-Silico Screening

Protein-ligand interactions: computational docking.

Integration of Ligand-Based Drug Screening with Structure-Based Drug Screening by Combining Maximum Volume Overlapping Score with Ligand Docking

Comparative study of the efficiency of three protein-ligand docking programs.

Drug Design for XRCC4 in Silico

1 application of a bioinformatics approach to high-throughput docking for drug discovery.

Target Prediction of 5,10,15,20-Tetrakis(4'-Sulfonatophenyl)-Porphyrin Using Molecular Docking.

A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening

In Silico Screening of Drugs That Target Different Forms of E Protein for Potential Treatment of COVID-19.

In Silico Drug Screening Based on a Protein-Compound Affinity Matrix

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Bioinformatics Based Ligand-Docking and in-Silico Screening

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Integration of Ligand-Based Drug Screening with Structure-Based Drug Screening by Combining Maximum Volume Overlapping Score with Ligand Docking

Comparative study of the efficiency of three protein-ligand docking programs.

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