:: DESCRIPTION
ScoreDotsAtAtom Bookkeep all-atom contact dots by each atom. Typically used to generate raw data for kincontours.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
ScoreDotsAtAtom is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
Using Autobondrot, Probe can generate multiple molecular conformations by rotating atoms around defined dihedral axes and perform other transformations. To use this function you must construct an input script defining rotatable bonds, etc. Usually called .rotscr files, they are quite similar to the @bondrot sections in a kinemage file. The probe command iterates over each conformation and generates a tabular output of the probe score and the conformation angles.
Atomic coordinates for specific conformations (in PDB format) can be output.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The usefulness of this is as described in Word et al. (2000) Protein Sci. 9, 2251-2259 {
PDF, 188KB}.
Autobondrot is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
NAcontacts is a perl script which will read a pdb file with hydrogens and write a table of contact information between nucleic acid bases in different layers.
NAContacts is a perl script which uses Probe to calculate a table of base-stacking areas and scores, either between base layers or between single bases. It operates on a nucleic acid PDB file with all H atoms (usually added with Reduce). To visualize the contacts quantified in the output table, look at the kinemage file that NAcontacts produces (or run Probe with “base” as the atom selection).
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
NAContacts is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
Flipkin works with Reduce, Probe and Prekin to help you decide the best “flip state” for asparagine, glutamine, and histidine. Flipkin will generate recommendations as to correct orientation, ‘flip’, of the sidechains of Asn, Gln and His. It will also generate kinemages of the flips and with all-atom contact dots for your selection of the best flip state. The newer version of this script uses perl; an older version using awk rather than perl is also available at right
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Flipkin is free software available under the terms of its own BSD-style license.
:: 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
ClashScore generate a percentile plot of ClashScore versus Resolution like that found in the X-Ray Verification Task Force’s recommendation to wwPDB.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
ClashScore is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
Picky is an oligo design program that alleviates long and monotonous calculations by identifying probes that are very unique and specific to sequence regions. These calculations are based on parameters inputted by the user including optimal probe length, ideal percentage of guanine and cytosine content, salt concentration and the maximum length to which a target sequence matches any non-target sequence.
PICKY allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. PICKY can also be used to analyze existing microarray probes and evaluate their design quality. Because PICKY uses rigorous whole genome-based thermodynamic screening to identify potential hydrogen binding sites of each probe, it can also be utilized to design short interference RNA (siRNA) for gene knockout applications and to discover possible targets of regulatory short RNAs (e.g., microRNAs or sRNAs). Picky has exceptional computational capability and is also user friendly.
::DEVELOPER
Complex Computation Laboratory
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Register for the free 64-bit Picky license.
Register for the free 32-bit Picky license.
If you find Picky useful to your research, please cite the Picky papers below that are most relevant to your work. If you have no preference, we recommend you cite the newest Shared Probe Design paper.
Shared probe design and existing microarray reanalysis using PICKY.
Chou HH.
BMC Bioinformatics. 2010 Apr 20;11:196.PMID: 20406469
Direct calibration of PICKY-designed microarrays.
Chou HH, Trisiriroj A, Park S, Hsing YI, Ronald PC, Schnable PS.
BMC Bioinformatics. 2009 Oct 23;10:347.PMID: 19849862
Picky: oligo microarray design for large genomes.
Chou HH, Hsia AP, Mooney DL, Schnable PS.
Bioinformatics. 2004 Nov 22;20(17):2893-902. Epub 2004 Jun 4.PMID: 15180932
:: DESCRIPTION
Bndlst reads a PDB format file and for each atom prints a list of covalent and H-bonded neighboring atoms, along with several atomic properties. It is useful in building scripts which process atomic structures.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
BndLst is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
AtVol performs atomic volume calculations by separating each atom from neighboring atoms where their van der Waals spheres join and performing Monte Carlo integration to estimate the volume.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
AtVol is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
Cluster is a simple unix C++ program that builds collections of interacting items from records containing interacting pairs or larger fragments. It is part of the algorithm used in Reduce to find H-bond “cliques”
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Cluster is free software available under the terms of its own BSD-style license.
