Servers & Software
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
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