Protein Analysis

Structure Analysis

• ASTRAL Compendium
  Provides databases and tools useful for analyzing protein structures
• BioMagResBank
  Search for structural information of proteins, peptides, and nucleic acids based on NMR spectroscopic data
• CATH
  Hierarchical classification of protein domain structures by class, architecture, topology and homologous superfamily
• CEMC
  Align multiple protein structures based on C-alpha coordinate distances, using combinatorial extension (CE) and Monte Carlo (MC) optimization methods
• DALI
  Compare protein structures in 3D. Submitted coordinates of a query protein structure are compared with those in the Protein Data Bank, and a multiple alignment of structural neighbors is generated
• DMAPS
  Search for pre-computed multiple structure alignments for protein chains in the Protein Data Bank (PDB)
• EMBL-EBI MSD
  Search macromolecular structure data in the Protein Data Bank (PDB) and other integrated bioinformatics data resources
• HSSP
  Search for information of aligned protein sequence families and their secondary and tertiary structures
• JPRED
  Predict secondary structure for an amino acid sequence
• ModBase
  A database of three-dimensional protein models calculated by comparative modeling
• MODELLER
  Conduct comparative protein structure modeling and analysis
• MyHits
  Annotate protein sequences and analyze their domains and signatures
• NCBI MMDB
  Find the 3D structure of a protein from MMDB through Entrez Structure
• NCBI VAST
  Compare 3D coordinates of a newly determined protein structure to those in the MMDB/PDB database
• PDB: Protein Data Bank
  Search or process 3-D structure data of large molecules of proteins and nucleic acids
• PDBsum
  Search for overview of every macromolecular structure deposited in the Protein Data Bank
• PredictProtein
  Predict protein structure from submitted amino acid sequences
• PyMol
  Visualization and modeling software for macromolecular structure
• SCOP
  Search for information on protein structure relationships
• Swiss-Model
  Search for annotated 3D protein structural information of proteins
• TOPS
  Search topological descriptions of protein structures and visualize folding topologies