Protein Structure
Protein domains
MyHits is a database devoted to protein domains that also has a collection of tools for investigating the relationship between protein sequences and domains/motifs. Tools include searching, motif scanning, alignment programs, and reformatting sequence files.
Protein visualization
Pymol: molecular visualization software ideal for rendering protein structures for presentations.
Protean 3D (Lasergene): simple 3D structure viewer that provides the annotated sequence, and secondary structure elements.
Protean 3D (Lasergene): simple 3D structure viewer that provides the annotated sequence, and secondary structure elements.
Homology modeling
SWISSMODEL: SWISS-MODEL is a fully automated protein structure homology-modelling server. In automatic mode, the target sequence needs to be specified, and the template and sequence alignment is generated by the program. If the template is already identified, an alignment of target and template sequences and the structure file can be uploaded for performing the homology modeling.
I-TASSER: (Iterative Threading ASSEmbly Refinement) predicts three-dimensional structure by detecting structure templates from the Protein Data Bank using fold recognition. Full-length structure models are constructed by reassembling structural fragments from threading templates using replica exchange Monte Carlo simulations. I-TASSER often is the top-performing method in the CASP competitions.
PHYRE2: (Protein Homology/AnalogY Recognition Engine) relies on profiles or hidden Markov models (HMMs). These profiles/HMMs capture the mutational propensity of each position in an amino acid sequence based on observed mutations in related sequences and can be thought of as an 'evolutionary fingerprint' of a particular protein. PHYRE2 scores very well in the CASP competitions of protein structure prediction.
I-TASSER: (Iterative Threading ASSEmbly Refinement) predicts three-dimensional structure by detecting structure templates from the Protein Data Bank using fold recognition. Full-length structure models are constructed by reassembling structural fragments from threading templates using replica exchange Monte Carlo simulations. I-TASSER often is the top-performing method in the CASP competitions.
PHYRE2: (Protein Homology/AnalogY Recognition Engine) relies on profiles or hidden Markov models (HMMs). These profiles/HMMs capture the mutational propensity of each position in an amino acid sequence based on observed mutations in related sequences and can be thought of as an 'evolutionary fingerprint' of a particular protein. PHYRE2 scores very well in the CASP competitions of protein structure prediction.
Structure analysis
PDBePISA: PDBePISA is an interactive tool for the exploration of macromolecular interfaces. Given a crystallographic structure, the structural and chemical properties of macromolecular surfaces and interfaces (with ligands or with other protein subunits) can be examined. Probable quaternary structures (assemblies) can also be predicted and analyzed.
