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.
BAM is a graphical user interface (GUI) application for building protein homooligomers and heterooligomers by means of comparative (homology) modeling. As input BAM accepts one to six different amino acid "Target" sequences. A list of available template protein complexes grouped by their domain architecture is provided during the modeling process. The architecture list is automatically sorted with the most similar domain content of the Target presented first. The template list indicates whether a proposed template complex contains any additional protein subunits not present in the target that may be of biological interest. Within 10-60 mins, the user can expect to build a homology model of a biologically active protein complex consisting of all or some input protein sequences.
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.
A Protein Sequence Culling Server that has several capabilities in producing subsets of sequences from larger sets.
ProtCid is a database of similar protein-protein interfaces in crystal structures of homologous proteins. Its main goal is to identify and cluster homodimeric and heterodimeric interfaces observed in multiple crystal forms of homologous proteins. Such interfaces, especially of non-identical proteins or protein complexes, have been associated with biologically relevant interactions.
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.