Kin2Dcont 1.8 & Kin3Dcont 1.12 – Produce Molecule Contour Map

Kin2Dcont 1.8 & Kin3Dcont 1.12

:: DESCRIPTION

Kin2Dcont and Kin3Dcont read value/coordinate lists to produce contour maps in kinemage format. Both scattered data and uniformly sampled data can be contoured. Kin2Dcont can also be used to produce contours in PostScript format.

They are used to generate 2D or 3D contour maps in kinemage format. The programs kin2Dcont and kin3Dcont produce contour plots from tables of values and their 2-D or 3-D coordinates. If the data is scattered in space, the programs can smooth it and produce what is essentially a histogram in two or three dimensions. Evenly sampled data values can also be contoured, as well as data which is periodic, for example when the dimensions are angles with 360 deg the same as 0 deg.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux/ MacOsX/SGI-irix/Sun-SPARC

:: DOWNLOAD

Kin2Dcont  & Kin3Dcont

:: MORE INFORMATION

Citation:

A Decomposable Algorithm for Contour Surface Display Generation, Michael J. Zyda, ACM Transactions on Graphics, Vol. 7, No. 2, April 1988, Pages 129-148.

Kin2Dcont  & Kin3Dcont are free softwares available under the terms of its own BSD-style license.

Dangle 0.63 – Read PDB File & Generate Geometric Measurement Table

Dangle 0.63

:: 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

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

Dangle

:: MORE INFORMATION

Dangle is free software available under the terms of its own BSD-style license.

Dang 1.8 – Read PDB File & Generate Geometric Measurement Table

Dang 1.8

:: 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

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux/Mac OsX/SGI-irix/Sun-SPARC

:: DOWNLOAD

Dang

:: MORE INFORMATION

Dang is free software available under the terms of its own BSD-style license.

Correlate 1.03 – Integrative Analysis of 2 Genomic Data Sets

Correlate 1.03

:: DESCRIPTION

Correlate is an Excel plug-in for performing an integrative analysis of two genomic data sets.

If two sets of assays (e.g. gene expression and DNA copy number) have been performed on the same set of patient samples then sparse CCA can be used to find a set of variables in assay 1 that is maximally correlated with a set of variables in assay 2.

::DEVELOPER

Sam Gross / Balasubramanian Narasimhan / Robert Tibshirani /Daniela Witten

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Correlate

:: MORE INFORMATION

paper: Witten DM, Tibshirani R, and T Hastie (2009) A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10(3): 515-534

Remediator 1.60 – Convert PDB Files between PDBv2.3 & PDBv3.2 Formats

Remediator 1.60

:: 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

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

Remediator

:: 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.

Suitename 0.3 – RNA Conformer

Suitename 0.3

:: DESCRIPTION

Suitename is a new C program that supports the ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development

From dihedral-angle input for a specific RNA structure (usually from Dangle), Suitename categorizes the RNA backbone geometry of each suite (the sugar-to-sugar version of a residue) either as an outlier (“!!”) or as belonging to one of the 53 defined conformer bins.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

Suitename

:: MORE INFORMATION

Suitename is free software available under the terms of its own BSD-style license.

RNABC 1.11 – RNA Backbone Correction

RNABC 1.11

:: DESCRIPTION

RNABC (RNA Backbone Correction) is designed for reducing the steric clashes in dinucleotides of existing RNA backbone structures. It first fixes the phosphate and base positions, which are the clearest parts in X-ray crystallography structure, and then reconstructs the remaining atoms of the dinucleotide using forward kinematics and conjugate gradient method. The input parameters, like bond lengths, bond angles, and sugar pucker types, are from canonical values or specified by users. The output results cluster the possible suite conformations (from base to base) without steric clashes.

::DEVELOPER

Xueyi Wang & Prof. Jack Snoeyink
Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

RNABC

:: MORE INFORMATION

RNABC is described in X. Wang, G. Kapral, L. Murray, D. Richardson, J. Richardson & J. Snoeyink. “RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone”. Journal Mathematical Biology (published January 2008, doi: 10.1007/s00285-007-0082)

RNABC is free software available under the terms of its own BSD-style license.

RDCvis 1.02 – Residual Dipolar Coupling Visualizer

RDCvis 1.02

:: DESCRIPTION

RDCvis (Residual Dipolar Coupling visualizer) is a system for generating visualizations of RDC data in their macromolecular structural context. RDCvis uses specifically formatted NMR data files and PDB structure files in order to calculate and draw RDC representations. It takes advantage of the flexibility of the Kinemage graphics language by outputting results directly to a kinemage file, or directly incorporating the RDC curves into a pre-existing kinemage.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

RDCvis

:: MORE INFORMATION

RDCvis is free software available under the terms of its own BSD-style license.

KinImmerse 0.5 – Translate Kinemage Files into Software for Virtual Environment

KinImmerse 0.5

:: DESCRIPTION

KinImmerse translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE.

In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Linux

:: DOWNLOAD

KinImmerse

:: MORE INFORMATION

For a detailed description see KinImmerse: Macromolecular VR for NMR ensembles.

KinImmerse is free software available under the terms of its own BSD-style license.

Prekin 6.51 – Prepares Kinemages Files from PDB-format Files

Prekin 6.51

:: DESCRIPTION

Prekin prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files, using either a choice of built-in scripts or a flexible user specification of options. Prekin can be run in either an interactive mode with option selection from dialog panes; or, it can be run in command-line fashion with all options specified at program invocation.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

Prekin

:: MORE INFORMATION

Prekin is free software available under the terms of its own BSD-style license.