Servers & Software

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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

DockStar - Structural modeling of multimolecular protein complexes

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

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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