:: DESCRIPTION
PDBtool is an integrated software for handling PDB file. This tool could parse the coordinate, do SEQRES-ATOM mapping, calculate secondary structure and solvent accessibility, compute conformational letter, and reconstruct missing residues.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PRI-Modeler (protein-RNA interaction modeler)analyzes the conformation of the RNA, calculates the hydrogen bond (H bond) and van der Waals interactions between amino acids and nucleotides, extracts secondary and tertiary RNA structure elements, and identifies the patterns of interactions between the proteins and RNAs. This paper presents PRI-Modeler and its application to the hydrogen bond and van der Waals interactions in the most representative set of protein-RNA complexes. The analysis reveals several interesting interaction patterns at various levels.
::DEVELOPER
Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kyungsook Han, Chirag Nepa
PRI-Modeler: Extracting RNA structural elements from PDB files of protein–RNA complexes
FEBS Lett. 2007 May 1;581(9):1881-90.
:: DESCRIPTION
TORSIONS is a simple program to read a PDB file and calculate backbone torsion angles. It calculates phi, psi and omega and can also calculate C-alpha pseudo-torsions.
::DEVELOPER
Andrew C.R. Martin’s Bioinformatics Group at UCL
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Reduce is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Reduce is described in Word, et al.(1999) “Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation” J. Mol. Biol. 285, 1735-1747. (
:: DESCRIPTION
RmscopII is a Tcl/Tk script responsible to redirect protein structure files (PDB files) or RasMol scripts to multiple RasMol sessions. It can be used as a web browser helper application or as a standalone program.
:: SCREENSHOTS
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Clashlist is a simple UNIX script which uses the awk facility along with the programs Probe and Cluster to build lists of van der Waals clashes from an input PDB-format molecular data file (with H atoms). These lists are organized such that collections of interacting residues are grouped together, sorted by the worst clash. For the purposes of this analysis, a clash is defined as a van der Waals overlap ≥ 0.4 Å.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
ClashList is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
Dangle an updated and more general version of our program Dang in that it reads coordinates from a Protein DataBank (PDB) coordinate file for either protein or nucleic acid and generates geometric measurements for each residue. It is different from Dang in that Dangle: is Java-based, includes the capability of reporting deviations from ideal geometry as well as measurement values, and has a very flexible input syntax for specified the measurements desired. Dangle output is given as colon-delimited values, one line per residue. It is designed for facile use in scripts, and is the usual source of input for Suitename, either to generate the data for MolProbity’s multi-criterion table or in individual command-line use.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Dangle is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
Dang reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each residue or base. In its most basic form, it writes out dihedral angles (phi, psi, chi) hence the name. The output is formated for easy parsing by awk, grep, sort and other UNIX utilities.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Dang is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
Remediator converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2). Remediator is available as a Perl or Python script. The scripts should work on any type of computing platform, as long as your operating system has the appropriate framework.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Remediator uses the remediated Chemical Component Dictionary as its “rosetta stone” for conversion.
Remediator is free software available under the terms of its own BSD-style license.
