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<?xml version="1.0"?>
<api>
  <query>
    <pages>
      <page pageid="6" ns="0" title="Servers &amp; Software">
        <revisions>
          <rev xml:space="preserve">== &lt;span style=&quot;color:blue&quot;&gt;Docking (rigid, symmetric, protein-protein, protein-drug, protein-DNA, protein-peptide)&lt;/span&gt; ==

[http://bioinfo3d.cs.tau.ac.il/PatchDock/ PatchDock] - Rigid Unbound Docking of Molecules
    
[http://bioinfo3d.cs.tau.ac.il/SymmDock/ SymmDock] - Prediction of Complexes with C&lt;sub&gt;n&lt;/sub&gt; Symmetry

[http://bioinfo3d.cs.tau.ac.il/CombDock/download/ CombDock] - COMBinatorial ssembly by mutiple DOCKing 

[http://bioinfo3d.cs.tau.ac.il/FireDock/ FireDock] - Refinement and re-scoring of rigid-body protein-protein docking solutions

[http://bioinfo3d.cs.tau.ac.il/FiberDock/ FiberDock] - Flexible backbone and side-chain refinement and re-scoring of 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/ParaDock ParaDock] - Rigid protein flexible DNA Docking

[http://bioinfo3d.cs.tau.ac.il/PepCrawler PepCrawler] - Refinement and binding-affinity estimation of peptide inhibitors

[http://bioinfo3d.cs.tau.ac.il/FlexDock/ FlexDock] - Prediction of protein interactions with large scale hinge motion in one of the docked molecules

[http://bioinfo3d.cs.tau.ac.il/Memdock/ Memdock] - Membrane Protein Docking Algorithm

[http://bioinfo3d.cs.tau.ac.il/PepWhisperer/ PepWhisperer] - Pep-Whisperer: Inhibitory Peptide Design

FunnGen - Accelerating Protein-Protein Complex Validation

+++ A tutorial for PatchDock, FireDock and SymmDock - [http://bioinfo3d.cs.tau.ac.il/tutorial.zip Download docking tutorial]

== &lt;span style=&quot;color:blue&quot;&gt;Protein Structural Alignment (pairwise, multiple, flexible)&lt;/span&gt; ==

[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
== &lt;span style=&quot;color:blue&quot;&gt;Comparison of Binding Sites and Interactions&lt;/span&gt; ==

[http://bioinfo3d.cs.tau.ac.il/SiteEngine/ SiteEngine] - Pairwise 3D Alignment of Binding Sites

[http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/ I2I-SiteEngine] - Pairwise 3D Alignment of Protein-Protein Interfaces

[http://bioinfo3d.cs.tau.ac.il/MultiBind/ MultiBind] - Multiple 3D Alignment of Binding Sites

[http://bioinfo3d.cs.tau.ac.il/mappis/ MAPPIS] - Multiple 3D Alignment of Protein-Protein Interfaces

[http://bioinfo3d.cs.tau.ac.il/RsiteDB/ RsiteDB] - Classification and prediction of protein RNA nucleotide interactions

== &lt;span style=&quot;color:blue&quot;&gt;Nucleic Acids&lt;/span&gt; ==

[http://bioinfo3d.cs.tau.ac.il/ARTS ARTS] - Alignment of RNA (DNA) Tertiary Structures


[http://bioinfo3d.cs.tau.ac.il/HARP HARP] - Geodesic Hashing Alignment of RNA Secondary Structures including Pseudoknots

== &lt;span style=&quot;color:blue&quot;&gt;Pharmacophore Detection&lt;/span&gt; ==
  
[http://bioinfo3d.cs.tau.ac.il/PharmaGist PharmaGist] - Multiple flexible alignment of small drug-like ligand molecules

== &lt;span style=&quot;color:blue&quot;&gt;Hinge Detection&lt;/span&gt; ==

[http://bioinfo3d.cs.tau.ac.il/HingeProt HingeProt] - Prediction of hinges in protein structure using Elastic Network Models

== &lt;span style=&quot;color:blue&quot;&gt;Protein Structure Prediction&lt;/span&gt; ==

[http://bioinfo3d.cs.tau.ac.il/FOBIA FOBIA] - Folding by hierarchical Assembly

[https://bioinfo3d.cs.tau.ac.il/AAnchor/ AAnchor] - CNN guided detection of anchor amino acids in high resolution cryo-EM density maps

== &lt;span style=&quot;color:blue&quot;&gt;Modelling of Multimolecular Complexes&lt;/span&gt; ==

[http://modbase.compbio.ucsf.edu/multifit MultiFit] - Fitting of multiple proteins into their assembly density map

[http://bioinfo3d.cs.tau.ac.il/SymmDock/ SymmDock] - Prediction of Complexes with C&lt;sub&gt;n&lt;/sub&gt; Symmetry

[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/CombDock/download/ CombDock] - COMBinatorial ssembly by mutiple DOCKing

[http://bioinfo3d.cs.tau.ac.il/DockStar DockStar] - Structural modeling of multimolecular protein complexes

== &lt;span style=&quot;color:blue&quot;&gt;Protein-peptide Interaction Design&lt;/span&gt; ==

[http://bioinfo3d.cs.tau.ac.il/PepCrawler PepCrawler] - Refinement and binding-affinity estimation of peptide inhibitors

[http://bioinfo3d.cs.tau.ac.il/PinaColada/ PinaColada] - Peptide-Inhibitor Ant Colony Ad-hoc Design Algorithm

[http://bioinfo3d.cs.tau.ac.il/PepMatch/ PepMatch] - Knowledge Based Design of Protein Binding Peptides


== &lt;span style=&quot;color:blue&quot;&gt;Geometric Deep Learning for Protein-Protein Interactions &lt;/span&gt; ==

[http://bioinfo3d.cs.tau.ac.il/ScanNet/ ScanNet] - ScanNet: An interpretable geometric deep learning model for structure-based protein binding site prediction</rev>
        </revisions>
      </page>
    </pages>
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</api>