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SCWRL4.0
SCWRL4.0 is the most recent version of the SCWRL program for prediction of protein side-chain conformations. SCWRL4.0 is based on an algorithm based on graph theory that solves the combinatorial problem in side-chain prediction more rapidly than many other available program. |
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MolIDE
MolIDE is an open-source cross-platform graphical environment for homology modeling. It implements the most frequently used steps involved in modeling:
sequence search, secondary structure prediction, multiple-round psiblast alignments, assisted alignment editing (integrating a template viewer and secondary structure prediction), side chain replacement and loop building. |
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ArboDraw
ArboDraw is a program for building and displaying phylogenetic trees of protein and nucleic acid sequences. It can import and display dendrogram files in Newick format (generated by MUSCLE, Phylip, clustalw, etc.). Among the key features are the ability to annotate sequences, and to select and color independently various parts of the tree. A very convenient annotation functionality allows the user to view annotations by placing the mouse above the sequence of interest. Edited and annotated files can be saved and restored at a later time. |
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PISCES
A Protein Sequence Culling Server that has several capabilities in producing subsets of sequences from larger sets.
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DashPDB
DashPDB is a Mac OS X Dashboard widget designed to give quick access to the RCSB Protein Data Bank. A single click downloads the PDB file or the biological unit file or opens the RCSB's webpage on the PDB entry entered. |
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ProtBuD
ProtBuD is a new database of asymmetric units (ASU) and biological
units (BU) from PDB and PQS, and uses SCOP and PSIBLAST to provide ASU and BU for all entries with proteins in particular superfamilies or families. It allows the user to search the SCOP database for a particular entry, retrieve the asymmetric and biological units for almost all related
proteins in the same SCOP category, compare side-by-side the biological units designated by PDB and PQS, analyze the protein interfaces, and download quickly and conveniently the structure files of interest. |
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BioDownloader
BioDownloader is a program for downloading and/or updating files from ftp/http servers. The program has unique features that are specifically designed to deal with bioinformatics data files and servers (large file sets, selective file retrieval, built-in download settings repository, wizard for post- download file processing, simultaneous download of multiple files).
Besides the intuitive BioDownloader's features that allow the user to use it out-of-the-box, provides the experienced user a vast set of fine-tunning options and advanced features.
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XML2PDB
XML2PDB is a command line program designed to extract the structure information (.pdb), sequence information ( .pdbaa, .pdbnt) and the correspondence between coordinate and sequence residue numbering (.sc) from the xml structure files. Source code and makefiles for each operating system are included in the distribution for users who may wish to extend the output of XML2PDB. |
