:: DESCRIPTION
Vivaldi is a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.
Hendrickx PM, Gutmanas A, Kleywegt GJ.
Proteins. 2013 Apr;81(4):583-91. doi: 10.1002/prot.24213
:: DESCRIPTION
COMPPDB is the desktop PDB superposition tool for Windows system
::DEVELOPER
Nagahama Institute of Bio-Science and Technology
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The CELLmicrocosmos MembraneEditor (CmME) interactively generates heterogeneous PDB-based membranes with varying lipid compositions and semi-automatic protein placement. Supports membrane patches and vesicles, microdomains as well as stacking of monolayer and/or bilayer membranes.
::DEVELOPER
the Bioinformatics / Medical Informatics department at Bielefeld University.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Chem Inf Model. 2011 May 23;51(5):1165-82. doi: 10.1021/ci1003619. Epub 2011 Apr 19.
CELLmicrocosmos 2.2 MembraneEditor: a modular interactive shape-based software approach to solve heterogeneous membrane packing problems.
Sommer B1, Dingersen T, Gamroth C, Schneider SE, Rubert S, Krüger J, Dietz KJ.
:: DESCRIPTION
ccPDB is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank.
Agrawal P, Patiyal S, Kumar R, Kumar V, Singh H, Raghav PK, Raghava GPS.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/bay142.
ccPDB: compilation and creation of data sets from Protein Data Bank.
Singh H, Chauhan JS, Gromiha MM; Open Source Drug Discovery Consortium, Raghava GP.
Nucleic Acids Res. 2012 Jan;40(Database issue):D486-9. doi: 10.1093/nar/gkr1150.
:: DESCRIPTION
RNApdbee is a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.
::DEVELOPER
The Bioinformatics Group, Poznan University of Technology.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2014 Apr 25. [Epub ahead of print]
RNApdbee–a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.
Antczak M1, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, Szachniuk M.
:: DESCRIPTION
ExSer facilitates an automated extraction of the amino acid sequence that encode for the secondary structural regions of a protein from the protein data bank (PDB) file.
::DEVELOPER
Dr. L. Arul (arulsra@gmail.com )
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Vignesh D, Daniel P, Raja N, Balasubramanian P, Arul L.
ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements.
Bioinformation. 2010 Mar 31; 4(9):390-1. PMID: 20975886; PMCID: PMC2951642
:: DESCRIPTION
CCR XP tries to automate the detection and analysis of such clusters in protein structures.CCR XP is made of two input modules. CCR XP lite can be accessed directly (see query form on top), by uploading a PDB coordinate data or entering a PDB code and CCRs using default parameter settings for all protein chains in the coordinate file will be returned. The server will automatically (1) Extract fasta file from atom records (2) Find aligned sequences and calculate conservation scores (3) Cluster conserved residues and (4) Report several other structural properties of each residue as well as whole clusters, including their solvent accessibility that will allow to distinguish potential interface clusters from stabilizing core residues.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W398-401. doi: 10.1093/nar/gkq360. Epub 2010 May 10.
CCRXP: exploring clusters of conserved residues in protein structures.
Ahmad S, Keskin O, Mizuguchi K, Sarai A, Nussinov R.
:: DESCRIPTION
CIFTr is an application program for translating files in mmCIF format into files in PDB format.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2002 Jan 1;30(1):245-8.
The Protein Data Bank: unifying the archive.
Westbrook J, Feng Z, Jain S, Bhat TN, Thanki N, Ravichandran V, Gilliland GL, Bluhm W, Weissig H, Greer DS, Bourne PE, Berman HM.
:: DESCRIPTION
SEQMOL (“sequences & molecules”) is an integrated sequence alignment and PDB structure analysis utility. It can be used to align multiple protein and DNA sequences, compute evolutionary attributes of multiple sequence alignments (such as sequence conservation, hydrophobicity conservation, conformational flexibility conservation, physical covariation, protein-protein interface, protein-RNA interface and protein-DNA interface propensity, and conservations thereof) and to map these features onto PDB files.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PDBQT converter can help you convert a batch of .pdb or .mol2 or a mix of these files to .pdbqt files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
