Servers & Software

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(Docking (rigid, symmetric, protein-protein, protein-drug, protein-DNA, protein-peptide))
(Protein Structure Prediction)
 
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== <span style="color:blue">Protein Structural Alignment (pairwise, multiple, flexible)</span> ==
 
 
[http://bioinfo3d.cs.tau.ac.il/gossip/ GOSSIP] -  Global Structural Superposition of Proteins 
 
 
[http://bioinfo3d.cs.tau.ac.il/TriangleMatchBeta/ TriangleMatch] - Pairwise Protein Structure Alignment based on Ca atoms. With P-value.
 
 
[http://bioinfo3d.cs.tau.ac.il/FlexProt/ FlexProt] - Pairwise Alignment of Flexible Protein Structures
 
 
[http://bioinfo3d.cs.tau.ac.il/MultiProt/ MultiProt] - Multiple Protein Structure Alignment
 
 
[http://bioinfo3d.cs.tau.ac.il/MASS MASS] - Multiple Protein Structure Alignment by Secondary Structures
 
 
[http://bioinfo3d.cs.tau.ac.il/staccato/ STACCATO] - Structure Based Multiple Sequence Alignment
 
 
 
== <span style="color:blue">Docking (rigid, symmetric, protein-protein, protein-drug, protein-DNA, protein-peptide)</span> ==
 
== <span style="color:blue">Docking (rigid, symmetric, protein-protein, protein-drug, protein-DNA, protein-peptide)</span> ==
  
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[http://bioinfo3d.cs.tau.ac.il/SymmRef/download.html SymmRef] - Flexible backbone and side-chain refinement and re-scoring of symmetric rigid-body protein-protein docking solutions
 
[http://bioinfo3d.cs.tau.ac.il/SymmRef/download.html SymmRef] - Flexible backbone and side-chain refinement and re-scoring of symmetric rigid-body protein-protein docking solutions
 
[http://bioinfo3d.cs.tau.ac.il/tutorial.zip Download docking tutorial] - A tutorial for PatchDock, FireDock and SymmDock
 
  
 
[http://bioinfo3d.cs.tau.ac.il/ParaDock ParaDock] - Rigid protein flexible DNA Docking
 
[http://bioinfo3d.cs.tau.ac.il/ParaDock ParaDock] - Rigid protein flexible DNA Docking
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[http://bioinfo3d.cs.tau.ac.il/Memdock/ Memdock] - Membrane Protein Docking Algorithm
 
[http://bioinfo3d.cs.tau.ac.il/Memdock/ Memdock] - Membrane Protein Docking Algorithm
  
[http://bioinfo3d.cs.tau.ac.il/FunnGen/ FunnGen] - Accelerating Protein-Protein Complex Validation
+
FunnGen - Accelerating Protein-Protein Complex Validation
  
== <span style="color:red">Comparison of Binding Sites and Interactions</span> ==
+
+++ A tutorial for PatchDock, FireDock and SymmDock - [http://bioinfo3d.cs.tau.ac.il/tutorial.zip Download docking tutorial]
 +
 
 +
== <span style="color:blue">Protein Structural Alignment (pairwise, multiple, flexible)</span> ==
 +
 
 +
[http://bioinfo3d.cs.tau.ac.il/gossip/ GOSSIP] -  Global Structural Superposition of Proteins 
 +
 
 +
[http://bioinfo3d.cs.tau.ac.il/TriangleMatchBeta/ TriangleMatch] - Pairwise Protein Structure Alignment based on Ca atoms. With P-value.
 +
 
 +
[http://bioinfo3d.cs.tau.ac.il/FlexProt/ FlexProt] - Pairwise Alignment of Flexible Protein Structures
 +
 
 +
[http://bioinfo3d.cs.tau.ac.il/MultiProt/ MultiProt] - Multiple Protein Structure Alignment
 +
 
 +
[http://bioinfo3d.cs.tau.ac.il/MASS MASS] - Multiple Protein Structure Alignment by Secondary Structures
 +
 
 +
[http://bioinfo3d.cs.tau.ac.il/staccato/ STACCATO] - Structure Based Multiple Sequence Alignment
 +
== <span style="color:blue">Comparison of Binding Sites and Interactions</span> ==
  
 
[http://bioinfo3d.cs.tau.ac.il/SiteEngine/ SiteEngine] - Pairwise 3D Alignment of Binding Sites
 
[http://bioinfo3d.cs.tau.ac.il/SiteEngine/ SiteEngine] - Pairwise 3D Alignment of Binding Sites
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[http://bioinfo3d.cs.tau.ac.il/RsiteDB/ RsiteDB] - Classification and prediction of protein RNA nucleotide interactions
 
[http://bioinfo3d.cs.tau.ac.il/RsiteDB/ RsiteDB] - Classification and prediction of protein RNA nucleotide interactions
  
== <span style="color:red">Nucleic Acids</span> ==
+
== <span style="color:blue">Nucleic Acids</span> ==
  
 
[http://bioinfo3d.cs.tau.ac.il/ARTS ARTS] - Alignment of RNA (DNA) Tertiary Structures
 
[http://bioinfo3d.cs.tau.ac.il/ARTS ARTS] - Alignment of RNA (DNA) Tertiary Structures
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[http://bioinfo3d.cs.tau.ac.il/HARP HARP] - Geodesic Hashing Alignment of RNA Secondary Structures including Pseudoknots
 
[http://bioinfo3d.cs.tau.ac.il/HARP HARP] - Geodesic Hashing Alignment of RNA Secondary Structures including Pseudoknots
  
== <span style="color:red">Pharmacophore Detection</span> ==
+
== <span style="color:blue">Pharmacophore Detection</span> ==
 
    
 
    
 
[http://bioinfo3d.cs.tau.ac.il/PharmaGist PharmaGist] - Multiple flexible alignment of small drug-like ligand molecules
 
[http://bioinfo3d.cs.tau.ac.il/PharmaGist PharmaGist] - Multiple flexible alignment of small drug-like ligand molecules
  
== <span style="color:red">Hinge Detection</span> ==
+
== <span style="color:blue">Hinge Detection</span> ==
  
 
[http://bioinfo3d.cs.tau.ac.il/HingeProt HingeProt] - Prediction of hinges in protein structure using Elastic Network Models
 
[http://bioinfo3d.cs.tau.ac.il/HingeProt HingeProt] - Prediction of hinges in protein structure using Elastic Network Models
  
== <span style="color:red">Protein Structure Prediction</span> ==
+
== <span style="color:blue">Protein Structure Prediction</span> ==
  
 
[http://bioinfo3d.cs.tau.ac.il/FOBIA FOBIA] - Folding by hierarchical Assembly
 
[http://bioinfo3d.cs.tau.ac.il/FOBIA FOBIA] - Folding by hierarchical Assembly
  
== <span style="color:red">Modelling of Multimolecular Complexes</span> ==
+
[https://bioinfo3d.cs.tau.ac.il/AAnchor/ AAnchor] - CNN guided detection of anchor amino acids in high resolution cryo-EM density maps
 +
 
 +
== <span style="color:blue">Modelling of Multimolecular Complexes</span> ==
  
 
[http://modbase.compbio.ucsf.edu/multifit MultiFit] - Fitting of multiple proteins into their assembly density map
 
[http://modbase.compbio.ucsf.edu/multifit MultiFit] - Fitting of multiple proteins into their assembly density map
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[http://bioinfo3d.cs.tau.ac.il/DockStar DockStar] - Structural modeling of multimolecular protein complexes
 
[http://bioinfo3d.cs.tau.ac.il/DockStar DockStar] - Structural modeling of multimolecular protein complexes
  
== <span style="color:red">Protein-peptide Interaction Design</span> ==
+
== <span style="color:blue">Protein-peptide Interaction Design</span> ==
  
 
[http://bioinfo3d.cs.tau.ac.il/PepCrawler PepCrawler] - Refinement and binding-affinity estimation of peptide inhibitors
 
[http://bioinfo3d.cs.tau.ac.il/PepCrawler PepCrawler] - Refinement and binding-affinity estimation of peptide inhibitors

Latest revision as of 08:24, 31 March 2019

Contents

Docking (rigid, symmetric, protein-protein, protein-drug, protein-DNA, protein-peptide)

PatchDock - Rigid Unbound Docking of Molecules

SymmDock - Prediction of Complexes with Cn Symmetry

CombDock - COMBinatorial ssembly by mutiple DOCKing

FireDock - Refinement and re-scoring of rigid-body protein-protein docking solutions

FiberDock - Flexible backbone and side-chain refinement and re-scoring of rigid-body protein-protein docking solutions

SymmRef - Flexible backbone and side-chain refinement and re-scoring of symmetric rigid-body protein-protein docking solutions

ParaDock - Rigid protein flexible DNA Docking

PepCrawler - Refinement and binding-affinity estimation of peptide inhibitors

FlexDock - Prediction of protein interactions with large scale hinge motion in one of the docked molecules

Memdock - Membrane Protein Docking Algorithm

FunnGen - Accelerating Protein-Protein Complex Validation

+++ A tutorial for PatchDock, FireDock and SymmDock - Download docking tutorial

Protein Structural Alignment (pairwise, multiple, flexible)

GOSSIP - Global Structural Superposition of Proteins

TriangleMatch - Pairwise Protein Structure Alignment based on Ca atoms. With P-value.

FlexProt - Pairwise Alignment of Flexible Protein Structures

MultiProt - Multiple Protein Structure Alignment

MASS - Multiple Protein Structure Alignment by Secondary Structures

STACCATO - Structure Based Multiple Sequence Alignment

Comparison of Binding Sites and Interactions

SiteEngine - Pairwise 3D Alignment of Binding Sites

I2I-SiteEngine - Pairwise 3D Alignment of Protein-Protein Interfaces

MultiBind - Multiple 3D Alignment of Binding Sites

MAPPIS - Multiple 3D Alignment of Protein-Protein Interfaces

RsiteDB - Classification and prediction of protein RNA nucleotide interactions

Nucleic Acids

ARTS - Alignment of RNA (DNA) Tertiary Structures


HARP - Geodesic Hashing Alignment of RNA Secondary Structures including Pseudoknots

Pharmacophore Detection

PharmaGist - Multiple flexible alignment of small drug-like ligand molecules

Hinge Detection

HingeProt - Prediction of hinges in protein structure using Elastic Network Models

Protein Structure Prediction

FOBIA - Folding by hierarchical Assembly

AAnchor - CNN guided detection of anchor amino acids in high resolution cryo-EM density maps

Modelling of Multimolecular Complexes

MultiFit - Fitting of multiple proteins into their assembly density map

SymmDock - Prediction of Complexes with Cn Symmetry

SymmRef - Flexible backbone and side-chain refinement and re-scoring of symmetric rigid-body protein-protein docking solutions

CombDock - COMBinatorial ssembly by mutiple DOCKing

DockStar - Structural modeling of multimolecular protein complexes

Protein-peptide Interaction Design

PepCrawler - Refinement and binding-affinity estimation of peptide inhibitors

PinaColada - Peptide-Inhibitor Ant Colony Ad-hoc Design Algorithm

PepMatch - Knowledge Based Design of Protein Binding Peptides

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