AutoAssign is a constraint-based expert system for automating the analysis of backbone resonance assignments using NMR spectra of small proteins. Originally developed in the Lisp programming language the current version of AutoAssign includes a C++ server supported for SGI computer systems, together with a graphical user interface implemented in Java for multiplatform use.
AutoProc is a suite of programs for the automatic generation of scripts for multidimensional protein NMR data processing and format conversion. The programs are written in Perl and make use of ASCII tables that the user can modify.
Basic Local Alignment Search Tool
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
CLC Free Workbench
CLC Free Workbench enables users to perform bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options. Some of the features are GenBank searching, including download facilities and full graphical overview; user-friendly graphical tools for viewing DNA, RNA, and protein sequences; full integration of data input, data management, calculations results, and data export; DNA, RNA, and protein alignment tools; reverse translation; restriction site analysis; and phylogenetic analyses.
Dedicated Comparative Sequence Editor: a multiple alignment editor. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment
DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins. You can export the results for visualization and further analysis (VRML, PDB, and MMTK object format).
(commercial) Epik is designed for accurate enumeration of ligand protonation states in biological conditions.
GRAMM is a program for protein docking. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules (no information about the binding sites is needed). The program performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules.
Learning, Observing and Outputting Protein Patterns is a program for potential optimization and alignments. LOOPP aligns sequence to sequence, sequence to structure, and structure to structure. It further enables the optimization of potentials and scoring functions for the above mentioned applications.
MSAProbs is an open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons and Probalign.
Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids, and is available for free from this site for researchers at academic and non profit-making institutions.
Protein ASsignment by Threshold Accepting.
Plasmidb is a frontend to a simple MySQL database, which itself contains information about projects in molecular biology. The focus is the data pertaining to bacterial plasmids, but also the protein sequences which are being worked on for a particular project, DNA sequences of target genes.
The PROtein Nmr TOol: was primarily designed to handle spectra of peptides and proteins, but has also been used to assign carbohydrates and nucleic acids
relax is designed for the study of the dynamics of proteins or other macromolecules though the analysis of NMR relaxation data. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, and the Lipari and Szabo model-free analysis.
SC_rate is a general method to evaluate the accuracy of protein sequence alignment with very low sequence identity.
SCWRL is a new version of the SCWRL program for prediction of protein side-chain conformations. SCWRL3.0 is based on a new algorithm based on graph theory that solves the combinatorial problem in side-chain prediction more rapidly than any other available program. SCWRL3.0 is more accurate than previous versions of SCWRL, while the new algorithm will allow for development of more sophisticated energy functions and for incorporation of side-chain flexibility around rotameric positions.
Simloc compares two conformation of a molecule and, by comparing the local environments of each bond, detects the one that are candidate for hinges. Once hinges have been identified (depending on a threshold parameter) the hinge bonds are deleted and the resulting fragments are superimposed to see if the RMS has decreased.
Swiss PDBViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
TALOS is a database system for empirical prediction of phi and psi backbone torsion angles using a combination of five kinds (HA, CA, CB, CO, N) of chemical shift assignments for a given protein sequence.
Trajectory eXplorer is a simple Biodesigner-like program working under Linux and Windows. The program allows reading a protein folding simulation trajectory (TRA file) and saving a single frame as a PDB file.
WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.