• VMD

  • Referenced in 89 articles [sw18651]
  • molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained...
  • PDB2PQR

  • Referenced in 34 articles [sw13087]
  • coordinates to molecular structures from the Protein Data Bank and the assignment of parameters...
  • PISCES

  • Referenced in 31 articles [sw16873]
  • sets of protein sequences from the Protein Data Bank (PDB) by sequence identity and structural ... substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists...
  • TM-align

  • Referenced in 15 articles [sw22248]
  • representative protein chains from the Protein Data Bank (PDB) with a sequence identity cutoff ... predicted by TASSER for solved non-homologous proteins in PDB. For both folded and misfolded...
  • ProTherm

  • Referenced in 9 articles [sw16247]
  • data through links between entries in Protein Data Bank, Protein Information Resource and SWISS‐PROT...
  • iPfam

  • Referenced in 8 articles [sw29349]
  • domain interactions found in the Protein Data Bank. The database iPfam, available at http://ipfam.org ... structures that are found in the Protein Data Bank, providing interaction data at the molecular ... independent development, improving data access and giving clearer separation between the protein family and interactions...
  • MDAnalysis

  • Referenced in 9 articles [sw17696]
  • Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written...
  • Naccess

  • Referenced in 8 articles [sw12485]
  • molecule from a standard Protein Data Bank (PDB) file input. The output includes a file...
  • BioMagResBank

  • Referenced in 5 articles [sw40765]
  • partner in the Worldwide Protein Data Bank (wwPDB). The BMRB archive consists of four main ... depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands ... original author depositions available from the Protein Data Bank, (iii) time-domain (raw) spectral data ... provides free access to all of these data. BMRB has tools for querying the archive...
  • BindingDB

  • Referenced in 7 articles [sw23141]
  • structural data are present in the Protein Data Bank. The BindingDB website supports a range ... similarity; protein sequence; ligand and protein names; affinity ranges and molecular weight. Data sets generated...
  • RONN

  • Referenced in 7 articles [sw16909]
  • protein sequences derived from the Protein Data Bank shows that, based on the probability excess...
  • DISCO

  • Referenced in 7 articles [sw13152]
  • performed on molecules taken from the Protein Data Bank database. For each molecule, given...
  • PDB-REPRDB

  • Referenced in 5 articles [sw26865]
  • representative protein chains from the Protein Data Bank (PDB). Started at the Real World Computing ... /pdbreprdb/. The current database includes 33 368 protein chains from 16 682 PDB entries ... which are excluded (a) DNA and RNA data, (b) theoretically modeled data, (c) short chains...
  • LIGPLOT

  • Referenced in 5 articles [sw16869]
  • protein-ligand complexes from standard Protein Data Bank file input The output is a colour ... show other types of interaction in proteins and nucleic acids. It was designed to facilitate...
  • pKNOT

  • Referenced in 4 articles [sw16874]
  • growing number of structures in the Protein Data Bank (PDB). Studies show that the knot ... both ligand binding and enzyme activity in proteins such as the chromophore-binding domain...
  • BetaSCP

  • Referenced in 3 articles [sw08772]
  • twenty test models selected from the Protein Data Bank...
  • EMPIAR

  • Referenced in 4 articles [sw19728]
  • structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D images are stored ... uses the fault-tolerant Aspera platform for data transfers. EMPIAR is based on input from ... workshops organized by the Protein Data Bank in Europe (PDBe) and the Open Microscopy Environment...
  • STRIDE

  • Referenced in 4 articles [sw33184]
  • user with atomic coordinates in the Protein Data Bank (PDB) format. A searchable database...
  • JenaLib

  • Referenced in 4 articles [sw33975]
  • structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database...
  • 3DNA

  • Referenced in 4 articles [sw21991]
  • Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel...