Servers & Software

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(Protein Structural Alignment (parwise, multiple, flexible))
(Docking (rigid, symmetric, protein-protein, protein-drug, protein-DNA, protein-peptide))
 
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== <span style="color:red">Protein Structural Alignment (pairwise, multiple, flexible)</span> ==
 
== <span style="color:red">Protein Structural Alignment (pairwise, multiple, flexible)</span> ==
  
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[http://bioinfo3d.cs.tau.ac.il/staccato/ STACCATO] - Structure Based Multiple Sequence Alignment
 
[http://bioinfo3d.cs.tau.ac.il/staccato/ STACCATO] - Structure Based Multiple Sequence Alignment
  
== <span style="color:red">Docking (rigid, symmetric, protein-protein, protein-drug)</span> ==
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== <span style="color:red">Docking (rigid, symmetric, protein-protein, protein-drug, protein-DNA, protein-peptide)</span> ==
  
 
[http://bioinfo3d.cs.tau.ac.il/PatchDock/ PatchDock] - Rigid Unbound Docking of Molecules
 
[http://bioinfo3d.cs.tau.ac.il/PatchDock/ PatchDock] - Rigid Unbound Docking of Molecules
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[http://bioinfo3d.cs.tau.ac.il/tutorial.zip Download docking tutorial] - A tutorial for PatchDock, FireDock and SymmDock
 
[http://bioinfo3d.cs.tau.ac.il/tutorial.zip Download docking tutorial] - A tutorial for PatchDock, FireDock and SymmDock
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[http://bioinfo3d.cs.tau.ac.il/ParaDock ParaDock] - Rigid protein flexible DNA Docking
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[http://bioinfo3d.cs.tau.ac.il/PepCrawler PepCrawler] - Refinement and binding-affinity estimation of peptide inhibitors
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[http://bioinfo3d.cs.tau.ac.il/FlexDock/ FlexDock] - Prediction of protein interactions with large scale hinge motion in one of the docked molecules
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[http://bioinfo3d.cs.tau.ac.il/Memdock/ Memdock] - Membrane Protein Docking Algorithm
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[http://bioinfo3d.cs.tau.ac.il/FunnGen/ FunnGen] - Accelerating Protein-Protein Complex Validation
  
 
== <span style="color:red">Comparison of Binding Sites and Interactions</span> ==
 
== <span style="color:red">Comparison of Binding Sites and Interactions</span> ==
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[http://bioinfo3d.cs.tau.ac.il/CombDock/download/ CombDock] - COMBinatorial ssembly by mutiple DOCKing
 
[http://bioinfo3d.cs.tau.ac.il/CombDock/download/ CombDock] - COMBinatorial ssembly by mutiple DOCKing
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[http://bioinfo3d.cs.tau.ac.il/DockStar DockStar] - Structural modeling of multimolecular protein complexes
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== <span style="color:red">Protein-peptide Interaction Design</span> ==
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[http://bioinfo3d.cs.tau.ac.il/PepCrawler PepCrawler] - Refinement and binding-affinity estimation of peptide inhibitors
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[http://bioinfo3d.cs.tau.ac.il/PinaColada/ PinaColada] - Peptide-Inhibitor Ant Colony Ad-hoc Design Algorithm

Latest revision as of 09:53, 21 February 2017

Contents

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

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

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

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

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

DARTS - Database 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

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

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