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Protein-nucleic acid docking software tools

Computational techniques can complement experimental approaches in elucidating protein–nucleic acid interactions. In particular, docking methods aim at predicting the three-dimensional (3D) structures of macromolecular complexes, starting from…
HADDOCK
Web

HADDOCK High Ambiguity Driven protein-protein DOCKing

An information-driven flexible docking approach for the modeling of…

An information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from…

PatchDock
Web
Desktop

PatchDock

Finds docking transformations that yield good molecular shape complementarity.…

Finds docking transformations that yield good molecular shape complementarity. A wide interface is ensured to include several matched local features of the docked molecules. PatchDock divides the…

TCP-seq
Desktop

TCP-seq translation complex profile sequencing

Uses fast covalent fixation of translation complexes in live cells, followed by…

Uses fast covalent fixation of translation complexes in live cells, followed by RNase footprinting of translation intermediates and their separation into complexes involving either the full ribosome…

NPDock
Web

NPDock Nucleic acid-Protein Dock

A web server for modeling of RNA-protein and DNA-protein complex structures.…

A web server for modeling of RNA-protein and DNA-protein complex structures. NPDock combines (1) GRAMM for global macromolecular docking, (2) scoring with a statistical potential, (3) clustering of…

Oli
Desktop

Oli

Represents three methods allowing the description of RNA sequences. Oli is the…

Represents three methods allowing the description of RNA sequences. Oli is the first method and uses tetranucleotides as features. OliMo is the second, and integrates motif scores from…

MORDOR
Desktop

MORDOR MOlecular Recognition with a Driven dynamics OptimizeR

Allows creation of binding site and docking. MORDOR is a software which…

Allows creation of binding site and docking. MORDOR is a software which contains all of the tools for virtual screening. The software can perform the main docking using its own energetic and…

RpveScore
Desktop

RpveScore

Consists of the pairwise potential and six physics-based energy terms.…

Consists of the pairwise potential and six physics-based energy terms. RpveScore is a weighted combined scoring function including physics based energy terms and the knowledge-based pairwise…

FTDock
Desktop

FTDock Fourier Transform rigid-body Docking

Discretises two molecules onto orthogonal grids and performs a global scan of…

Discretises two molecules onto orthogonal grids and performs a global scan of translational and rotational space. In order to scan rotational space it is necessary to rediscretise one of the…

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