• VMD

  • Referenced in 72 articles [sw18651]
  • molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained...
  • PDB2PQR

  • Referenced in 29 articles [sw13087]
  • coordinates to molecular structures from the Protein Data Bank and the assignment of parameters...
  • PISCES

  • Referenced in 18 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 13 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...
  • Naccess

  • Referenced in 6 articles [sw12485]
  • molecule from a standard Protein Data Bank (PDB) file input. The output includes a file...
  • BindingDB

  • Referenced in 4 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...
  • BetaSCP

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

  • Referenced in 4 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...
  • RONN

  • Referenced in 4 articles [sw16909]
  • protein sequences derived from the Protein Data Bank shows that, based on the probability excess...
  • pKNOT

  • Referenced in 3 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...
  • CUPSAT

  • Referenced in 3 articles [sw16877]
  • requires the protein structure in Protein Data Bank format and the location of the residue ... angles), and comprehensive information about changes in protein stability for 19 possible substitutions...
  • LIGPLOT

  • Referenced in 3 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...
  • ParCrys

  • Referenced in 3 articles [sw16920]
  • produce diffraction-quality crystals. The Protein Data Bank (PDB) provided training data whilst the databases...
  • QTM

  • Referenced in 3 articles [sw14198]
  • from atomic resolution data in the Protein Data Bank (PDB). A smooth volumetric electron density...
  • MDAnalysis

  • Referenced in 3 articles [sw17696]
  • Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written...
  • DISCO

  • Referenced in 3 articles [sw13152]
  • performed on molecules taken from the Protein Data Bank database. For each molecule, given...
  • PIBASE

  • Referenced in 2 articles [sw29350]
  • interfaces. Motivation: In recent years, the Protein Data Bank (PDB) has experienced rapid growth ... utility of the high resolution proteinprotein interaction data stored in the PDB, we have...
  • DBAli tools

  • Referenced in 2 articles [sw16872]
  • structural information deposited in the Protein Data Bank (PDB). These tools include (i) the DBAlit ... input the 3D coordinates of a protein structure for comparison by MAMMOTH against all chains...
  • FRASS

  • Referenced in 2 articles [sw15707]
  • database derived from the Protein Data Bank. We observed that FRASS scores correlate well with...