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Related Links for PDBSiteScanTool Content

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Found 36 links

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3D-FunTool Content

http://3dfun.bioinfo.pl [open in a new window]

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Protein > 3-D Structure Comparison
Protein > Annotation and Function

3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
3D-Fun: predicting enzyme function from structure20086
NAR Web Server Issue 2008
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tagsalgorithms enzymes molecular models protein structural homology

AS2TSTool Content

http://as2ts.llnl.gov/ [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction

The AS2TS (Amino acid Sequence to Tertiary Structure) system consists of servers for protein structure analysis and modelling.

links directory index: 410
TitlePublication YearGoogle Scholar Citation Count
AS2TS system for protein structure modeling and analysis200524
LGA: A method for finding 3D similarities in protein structures2003386
NAR Web Server Issue 2003NAR Web Server Issue 2005
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tagsalgorithms biomolecular nuclear magnetic resonance proteins sequence alignment

BSDDDatabase Content

http://iris.physics.iisc.ernet.in/bsdd/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.

This content is being maintained by kitty.pillai.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BSDD: Biomolecules Segment Display Device--a web-based interactive display tool20041
NAR Web Server Issue 2004
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tagsamino acid motifs molecular models molecular structure proteins

CRASPTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/ [open in a new window]

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Sequence Comparison > Analysis of Aligned Sequences

Correlation analysis of the amino acid substitutions in protein sequences (CRASP) takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest dependent evolution of functionally related pairs of amino acids.

links directory index: 34
TitlePublication YearGoogle Scholar Citation Count
CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences200434
NAR Web Server Issue 2004
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eF-seekTool Content

http://ef-site.hgc.jp/eF-seek/index.jsp [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.

This content is being maintained by Kenta Nakai.

links directory index: 409
TitlePublication YearGoogle Scholar Citation Count
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape200727
Identification of the ligand binding sites on the molecular surface of proteins200547
eF-site and PDBjViewer: database and viewer for protein functional sites200472
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site2003118
Protein informatics towards function identification200352
Identification of protein functions from a molecular surface database, eF-site200293
NAR Web Server Issue 2007
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tagsalgorithms antibodies binding sites biological models computational biology computer simulation database management systems ligands molecular models protein conformation protein databases protein folding proteins proteomics s-adenosylhomocysteine static electricity structure-activity relationship three-dimensional imaging trypsin

FeatureMap3DTool Content

http://www.cbs.dtu.dk/services/FeatureMap3D/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching and Classification

FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB200611
NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology amino acids conserved sequence exons molecular models protein conformation protein databases protein structural homology proteins sequence alignment

firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php [open in a new window]

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Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

links directory index: 128
TitlePublication YearGoogle Scholar Citation Count
firestar--advances in the prediction of functionally important residues20112
FireDB--a database of functionally important residues from proteins of known structure200730
firestar--prediction of functionally important residues using structural templates and alignment reliability200744
SQUARE--determining reliable regions in sequence alignments200452
NAR Web Server Issue 2007NAR Web Server Issue 2011
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GlyprotTool Content

http://www.glycosciences.de/modeling/glyprot/php/main.php [open in a new window]

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Other Molecules > Carbohydrates
Protein > 3-D Structural Features

Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure.

This content is being maintained by luetteke.

links directory index: 62
TitlePublication YearGoogle Scholar Citation Count
GlyProt: in silico glycosylation of proteins200562
NAR Web Server Issue 2005
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tagscomputational biology glycoproteins glycosylation humans molecular models protein conformation protein isoforms

I2I-SiteEngineTool Content

http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Networks & Interactions, Pathways and Enzymes

Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.

links directory index: 62
TitlePublication YearGoogle Scholar Citation Count
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces200538
BioInfo3D: a suite of tools for structural bioinformatics200424
NAR Web Server Issue 2005
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MEDockTool Content

http://medock.csie.ntu.edu.tw/ [open in a new window]

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Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

MEDock (Maximum-Entropy based Docking) is a tool for predicting ligand binding sites.

This content is being maintained by dirty.

links directory index: 34
TitlePublication YearGoogle Scholar Citation Count
MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm200534
NAR Web Server Issue 2005
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tagsalgorithms binding sites computer simulation dna drug design entropy ligands molecular models pharmaceutical preparations proteins

MeMoTool Content

http://www.bioinfo.tsinghua.edu.cn/%7Etigerchen/memo.html [open in a new window]

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Protein > Sequence Features

Methylation Modification Prediction Server (MeMo) is a server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM).

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
MeMo: a web tool for prediction of protein methylation modifications200641
NAR Web Server Issue 2006
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tagsarginine artificial intelligence lysine methylation post-translational protein processing proteins

MINERTool Content

http://coit-apple01.uncc.edu/MINER/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

MINER is a tool for the identification and visualization of phylogenetic motifs (regions within a multiple sequence alignment (MSA) that conserve the overall phylogeny of the complete family).

links directory index: 69
TitlePublication YearGoogle Scholar Citation Count
MINER: software for phylogenetic motif identification200517
Predicting protein functional sites with phylogenetic motifs200552
NAR Web Server Issue 2005
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tagsamino acid motifs base sequence binding sites chemical models computational biology conserved sequence cytochrome p-450 enzyme system false positive reactions fungal proteins molecular evolution molecular models phylogeny protein binding protein conformation protein databases protein sequence analysis proteins proteomics saccharomyces cerevisiae sequence alignment succinate dehydrogenase

MMDBDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Sequence Data

Molecular Modelling Database of 3-D structures; experimentally determined structures only.

links directory index: 165
TitlePublication YearGoogle Scholar Citation Count
MMDB: 3D structures and macromolecular interactions20122
MMDB: Entrez's 3D-structure database2003163
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external linksLink on Wikipedia
tagsanimals molecular models protein databases protein structural homology proteins tertiary protein structure three-dimensional imaging

PBSwordTool Content

http://pbs.rnet.missouri.edu [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

PBSword is a web server designed for efficient and accurate comparisons and searches of geometrically similar protein-protein binding sites from a large-scale database.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2012
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pevoSOARTool Content

http://sts.bioengr.uic.edu/pevosoar/ [open in a new window]

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Protein > 3-D Structure Comparison

pvSOAR takes a PDB ID or structure file as input, and searches for other proteins with surface regions that are similar to the query structure.

links directory index: 55
TitlePublication YearGoogle Scholar Citation Count
pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins200455
NAR Web Server Issue 2004
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tagsamino acids binding sites molecular models protein conformation protein databases proteins

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