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Protein Bioinformatics

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Cover of 'Protein Bioinformatics'

Table of Contents

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    Book Overview
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    Chapter 1 Protein Bioinformatics Databases and Resources
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    Chapter 2 UniProt Protein Knowledgebase
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    Chapter 3 Tutorial on Protein Ontology Resources
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    Chapter 4 CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences
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    Chapter 5 Structure-Based Virtual Screening
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    Chapter 6 Bioinformatics Analysis of Protein Phosphorylation in Plant Systems Biology Using P3DB
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    Chapter 7 Navigating the Glycome Space and Connecting the Glycoproteome
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    Chapter 8 Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins
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    Chapter 9 Analysis of Cysteine Redox Post-Translational Modifications in Cell Biology and Drug Pharmacology
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    Chapter 10 Analysis of Protein Phosphorylation and Its Functional Impact on Protein–Protein Interactions via Text Mining of the Scientific Literature
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    Chapter 11 Functional Interaction Network Construction and Analysis for Disease Discovery
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    Chapter 12 Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information
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    Chapter 13 NDEx: A Community Resource for Sharing and Publishing of Biological Networks
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    Chapter 14 Bioinformatics Analysis of Functional Associations of PTMs
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    Chapter 15 Bioinformatics Analysis of PTM-Modified Protein Interaction Networks and Complexes
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    Chapter 16 iPTMnet: Integrative Bioinformatics for Studying PTM Networks
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    Chapter 17 Protein Identification from Tandem Mass Spectra by Database Searching
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    Chapter 18 Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite
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    Chapter 19 Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry: Data to Knowledge Pipelines
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    Chapter 20 Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks
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    Chapter 21 Computational and Statistical Methods for High-Throughput Mass Spectrometry-Based PTM Analysis
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    Chapter 22 Cross-Species PTM Mapping from Phosphoproteomic Data
Attention for Chapter 5: Structure-Based Virtual Screening
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Citations

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Chapter title
Structure-Based Virtual Screening
Chapter number 5
Book title
Protein Bioinformatics
Published in
Methods in molecular biology, February 2017
DOI 10.1007/978-1-4939-6783-4_5
Pubmed ID
Book ISBNs
978-1-4939-6781-0, 978-1-4939-6783-4
Authors

Qingliang Li, Salim Shah

Editors

Cathy H. Wu, Cecilia N. Arighi, Karen E. Ross

Abstract

Structure-based virtual screening (SBVS) is a computational approach used in the early-stage drug discovery campaign to search a chemical compound library for novel bioactive molecules against a certain drug target. It utilizes the three-dimensional (3D) structure of the biological target, obtained from X-ray, NMR, or computational modeling, to dock a collection of chemical compounds into the binding site and select a subset of these compounds based on the predicted binding scores for further biological evaluation. In the present work, we illustrate the basic process of conducting a SBVS with examples using freely accessible tools and resources.

Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 122 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 122 100%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 17 14%
Student > Ph. D. Student 15 12%
Student > Master 14 11%
Researcher 10 8%
Student > Doctoral Student 4 3%
Other 13 11%
Unknown 49 40%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 20 16%
Chemistry 14 11%
Pharmacology, Toxicology and Pharmaceutical Science 12 10%
Computer Science 7 6%
Agricultural and Biological Sciences 6 5%
Other 10 8%
Unknown 53 43%