(Q57234936)

1

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Pantelis G. Bagos

object named as

Pantelis Bagos

4

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author name string

Ernesto Iacucci

2

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Ioannis Iliopoulos

Announcing the worldwide Protein Data Bank

3

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publication date

2013

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page(s)

79-100

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cites work

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Visualization of macromolecular structures.

31 March 2020

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The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

31 March 2020

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Visualizing the future of molecular graphics

31 March 2020

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Visualization software for molecular assemblies

31 March 2020

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The kinemage: A tool for scientific communication

31 March 2020

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UCSF Chimera--a visualization system for exploratory research and analysis

31 March 2020

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The SRS 3D module: integrating structures, sequences and features

31 March 2020

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STRAP: editor for STRuctural Alignments of Proteins

31 March 2020

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Exploring DNA structure with Cn3D.

31 March 2020

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Cn3D: sequence and structure views for Entrez

31 March 2020

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Cn3D: a new generation of three-dimensional molecular structure viewer

31 March 2020

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Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective.

31 March 2020

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SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

31 March 2020

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An extensively modified version of MolScript that includes greatly enhanced coloring capabilities

31 March 2020

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A component-based software environment for visualizing large macromolecular assemblies

31 March 2020

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VMD: visual molecular dynamics

31 March 2020

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Raster3D Version 2.0. A program for photorealistic molecular graphics

31 March 2020

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MOLMOL: a program for display and analysis of macromolecular structures

31 March 2020

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Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels

31 March 2020

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THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

31 March 2020

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ProSAT2--Protein Structure Annotation Server.

31 March 2020

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The IMB Jena Image Library of Biological Macromolecules: 2002 update

31 March 2020

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Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature

31 March 2020

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WHAT IF: a molecular modeling and drug design program

31 March 2020

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Utilising structural knowledge in drug design strategies: applications using Relibase.

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

SuperLigands - a database of ligand structures derived from the Protein Data Bank

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

tCONCOORD-GUI: visually supported conformational sampling of bioactive molecules

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Protein flexibility and dynamics using constraint theory

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

MovieMaker: a web server for rapid rendering of protein motions and interactions

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

The Database of Macromolecular Motions: new features added at the decade mark

31 March 2020

1 reference

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NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Anisotropic network model: systematic evaluation and a new web interface

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

A reference guide for tree analysis and visualization

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Gene ontology: tool for the unification of biology

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

The Unified Medical Language System (UMLS): integrating biomedical terminology

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Modernizing the tree of life

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Transformation and normalization of oligonucleotide microarray data

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Microarray data normalization and transformation

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Hierarchical clustering schemes

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Neighbor-joining revealed.

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

MUSCLE: multiple sequence alignment with high accuracy and high throughput

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Basic local alignment search tool

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

T-Coffee: A novel method for fast and accurate multiple sequence alignment

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Extended Newick: it is time for a standard representation of phylogenetic networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

NEXUS: an extensible file format for systematic information

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

phyloXML: XML for evolutionary biology and comparative genomics

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Visualization of multiple alignments, phylogenies and gene family evolution

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Tree visualization with tree-maps: 2-d space-filling approach

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Space, time, form: viewing the Tree of Life

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

ATV: display and manipulation of annotated phylogenetic trees

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Visualizations for taxonomic and phylogenetic trees

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Visualizing large hierarchical clusters in hyperbolic space

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Visualising very large phylogenetic trees in three dimensional hyperbolic space

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

TreeDyn: towards dynamic graphics and annotations for analyses of trees

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

TreeVector: scalable, interactive, phylogenetic trees for the web

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Dendroscope: An interactive viewer for large phylogenetic trees

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Paloverde: an OpenGL 3D phylogeny browser

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Phylogeographic information systems: putting the geography into phylogeography

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Geophylogenies and the Map of Life

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Search for a 'Tree of Life' in the thicket of the phylogenetic forest

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Finishing the euchromatic sequence of the human genome

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Initial sequencing and analysis of the human genome

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Genome sequencing in microfabricated high-density picolitre reactors

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Network medicine: a network-based approach to human disease

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Mutational derivatives of PhiC31 integrase with increased efficiency and specificity

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

High-resolution mapping of copy-number alterations with massively parallel sequencing

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

rSW-seq: algorithm for detection of copy number alterations in deep sequencing data

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

RNA-Seq: a revolutionary tool for transcriptomics

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Genome-wide mapping of in vivo protein-DNA interactions

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

A map of human genome variation from population-scale sequencing

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

The International HapMap Project Web site

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Integrating ethics and science in the International HapMap Project

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

The International HapMap Project

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

The Ensembl Web site: mechanics of a genome browser

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Mining the draft human genome

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

The human genome browser at UCSC

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Using graph theory to analyze biological networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

The tandem affinity purification (TAP) method: a general procedure of protein complex purification

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

A comprehensive two-hybrid analysis to explore the yeast protein interactome

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Functional organization of the yeast proteome by systematic analysis of protein complexes

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Phage display: practicalities and prospects

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

An automated method for finding molecular complexes in large protein interaction networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

jClust: a clustering and visualization toolbox

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Protein complexes and functional modules in molecular networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Development and implementation of an algorithm for detection of protein complexes in large interaction networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Complex discovery from weighted PPI networks.

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

A structural approach for finding functional modules from large biological networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

CFinder: locating cliques and overlapping modules in biological networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

GIBA: a clustering tool for detecting protein complexes

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Using indirect protein-protein interactions for protein complex prediction.

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Combining functional and topological properties to identify core modules in protein interaction networks.

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Semantic integration to identify overlapping functional modules in protein interaction networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Growing functional modules from a seed protein via integration of protein interaction and gene expression data

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

A Max-Flow-Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Identification of functional modules using network topology and high-throughput data

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Computational approaches for detecting protein complexes from protein interaction networks: a survey

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

A survey of visualization tools for biological network analysis

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Visualization of omics data for systems biology

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Tools for visually exploring biological networks.

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Graph-based analysis and visualization of experimental results with ONDEX

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Cytoscape: a software environment for integrated models of biomolecular interaction networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Medusa: A tool for exploring and clustering biological networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology.

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

iPath: interactive exploration of biochemical pathways and networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Presenting and exploring biological pathways with PathVisio

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

EXPANDER--an integrative program suite for microarray data analysis

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

An interactive power analysis tool for microarray hypothesis testing and generation

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Expression Profiler: next generation--an online platform for analysis of microarray data

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Arena3D: visualizing time-driven phenotypic differences in biological systems

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Arena3D: visualization of biological networks in 3D.

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Construction, visualisation, and clustering of transcription networks from microarray expression data

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Proteome survey reveals modularity of the yeast cell machinery

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Exploration of biological network centralities with CentiBiN.

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6

Visualizing biological data-now and in the future

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-00375-7_6