Structural Analysis HOME Comparison & Alignments Functional Analysis Structural Analysis Other Analytical Tools
123D+ A program which combines substitution matrix, secondary structure prediction, and contact capacity potentials to thread a sequence through the set of structures.
3D-PSSM A fast, web-based method for protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure and solvation potential information.
3D-Doc Suite This Suite of tools contains: FTDock, RPScore and MultiDock. FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information. FTDock implements the Fourier correlation algorithm of Katchalski-Katzir and coworkers plus an electrostatics function amenable to Fourier correlation. RPScore ( Residue level Pair potential Score ) uses a single distance constraint empiricaly derived pair potential to screen the ouptut from FTDock. It has been shown that this can reduce dramatically the list of possible complexes within which can be found a correct solution. This program is fully integrated with the present version of FTDock. A further improvement in the quality of the predictions can be gained by using MultiDock (Multiple copy side-chain refinement Dock ).
ABS: Analytical Biostatistics Section Prediction of secondary structures.
Atlas of Protein Side-Chain Interactions This atlas depicts how amino acid side-chains pack against one another within the known protein structures. This packing, which is governed by the interactions between the 20 different types of side-chains, determines the structure, function, and stability of proteins.
AutoDock A suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
Bioinformatics Links Directory Features curated links to molecular resources, tools and databases. All of the resources are well tested and are either free or available for a nominal fee. The links listed in this directory are selected on the basis of recommendations from bioinformatics experts in the field. All links contained in the NAR Webserver issue since 2003 are also listed.
BIOTOOLKIT Hundreds of advanced online tools for molecular biology data retrieval, analysis, and visualization. Also provides annotated links to web tools for the study of nucleic acid, genome, and protein structure.
BTPRED: Beta-Turn Prediction Server A fast method for predicting the location and type of beta-turns in protein sequences. It also predicts whether or not a predicted beta-turn is type I or type II.
CBS_CPHmodels A collection of methods and databases developed to predict protein structures. It currently consists of the following tools: CPHmodels: predicts protein structure using comparative (homology) modeling, distanceP, a neural network based method to predict contacts between C-alpha atoms from the amino acid sequence, RedHom: a tool to find a subset with low sequence similarity in a database.
CBS_TMHMM Prediction of transmembrane helices in proteins.
CDART: Conserved Domain Architecture Retrieval Tool (NCBI) Find a protein sequence's domain architecture.
Cn3D A viewing and analysis program that provides linked sequence and three-dimensional displays of the macromolecular structures and VAST alignments of protein domains accessible through NCBI's MMDB (Molecular Modeling DataBase). Cn3D can be used in a standalone mode or configured to work as a helper application for Entrez where it facilitates rapid 3D visualization and comparison of macromolecular structures.
EMBL_Dali A network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank.
EMBOSS "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
EMBOSS Sequence Analysis Servers A suite of free software tools for sequence analysis, including that of GCG. There are a wide variety of programs that make up the suite, ranging in application from database searching to presentation of sequence data.
ESPript 1.8 A program for analysis of protein sequences, multiple alignments, structural predictions, and more.
ExPASy: Expert Protein Analysis System This server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.
ExPASy_SWISS-MODEL An automated protein modeling server. The purpose of this server is to make Protein Modeling accessible to all biochemists and molecular biologists World Wide.
ExPASy_SWISS-PDB Viewer An application that provides a user friendly interface allowing to analyze 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.
Folding@Home Distributed Computing A distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. The project uses novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved.
GCG: Genetics Computer Group It enables scientists to analyze DNA and protein sequences by editing, mapping, comparing, and aligning them. Other programs facilitate RNA secondary structure prediction, DNA fragment assembly, and evolutionary analysis. GCG serves molecular biologists by building practical tools that implement the important techniques of mathematical biology.
GenomeAtlas The DNA Structural Atlas is a method of visualizing structural features within large regions of DNA. It was originally designed for analysis of complete genomes, but can also be used quite readily for analysis of regions of DNA as small as a few thousand bp in length.
JAMBW: Java-based Molecular Biology Workbench The programs and documentation have been put together in order to try to give a free access to the exploitment of the most common bioinformatics operations that a molecular biologist currently has.
Mfold: The European mfold Server A set of programs that uses dynamic programming to predict RNA secondary structures by free energy minimization. It can also predict DNA secondary structures using the free energies.
Molecular Modeling at UMDNJ Academic Computing Services supports a suite of molecular modeling products at UMDNJ.
NCBI-VAST: Vector Alignment Search Tool Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the domains in MMDB is compared to every other one.
NCBI-Structure Group: The NCBI Structure Group maintains MMDB, a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis.
Paircoil Scoring Form This program predicts the location of coiled-coil regions in amino acid sequences.
PaRNAss: Prediction of Alternative RNA Secondary Structures A software approach to the prediction of structural switching, such as a reversible change of conformation as with an RNA molecule.
PDB Highlight For Substructure Visualization PDB highlight was developed for simple and powerful visualization of protein substructure in PDB.
PESTfind Analysis To objectively determine whether a protein contains a PEST region. The algorithm defines PEST sequences as hydrophilic stretches of amino acids greater than or equal to 12 residues in length.
PRED2D: Consensus structural prediction based on many analysis tools. "PRED2D launches DSC, PSIPRED, SIMPA96, NETASA, TMAP, TMPRED, NCOILS, and SEG to predict the secondary structure, the solvent exposure, the transmembrane segments, the coiled-coil and low-complexity regions of the input protein sequence."
Predict Protein e-mail Server An e-mail service to which you send an amino acid sequence and which sends back by return mail a prediction of the secondary structure.
Prof Secondary structure prediction. Descendant of the popular DSC program.
PAT: Protein Analysis Tool Kit An integrated bio-computing server. The main goal of is to facilitate the combination of different processing tools for more complex protein analyses. Tools cover the following topics: Primary sequence analysis Sequence similarity search Sequence alignment Sequence motif search Phylogeny Secondary structure prediction Non globular structure prediction Solvent accessibility prediction Tertiary structure analysis Tertiary structure display Tertiary structure superposition Tertiary structure modeling Tertiary structure evaluation Cellular localization Output format
Protein Explorer: Molecular Visualization Freeware Free software for looking at molecular structures. Protein Explorer is much easier and faster than Rasmol
Protein Hydrophilicity/Hydrophobicity Search and Comparison Server Provides tools for plotting, comparing and searching a library for similarities, of a protein's hydropathy profile.
PSA: Protein Structure Prediction Server Predicts probable secondary structures and folding classes for a given amino acid sequence.
PSIPRED: Protein Structure Prediction Server This "server allows you to submit a protein sequence, perform a prediction of your choice and receive the results of the prediction via e-mail. You may select one of three prediction methods to apply to your sequence: PSIPRED - a highly accurate method for protein secondary structure prediction MEMSAT3 - widely used transmembrane topology prediction method GenTHREADER - a sequence profile based fold recognition method"
QGRS Mapper A web-based server for predicting G-quadruplexes in nucleotide sequences.
RasMol & Chime: Molecular Visualization Freeware RasMol and Protein Explorer free software for looking at molecular structures. Chime shows molecules like RasMol, but unlike RasMol, Chime shows molecules inside a web page. Protein Explorer is much easier and faster than Rasmol
RNA Movies A system for the visualization of RNA secondary structure spaces. Its input is a script consisting of primary and secondary structure information. From this script, the system generates animated graphical structure representations.
SAINT: Structure Assignment with Instructive Transparency A heuristic-based method for the prediction of protein secondary-structure from a family of aligned, homologous sequences.
SAWTED: Structure Assignment with Text Description A method to improve the coverage of the detection of remote homologues of known structure by sequence searches and fold recognition programs. SAWTED uses an algorithm to compare the text of SWISS-PROT annotations related to the query and to the poor scoring hits. A single E-value is given for the user to assess the similarity of function.
Sequences Annotated By Structure A tool to apply structural information to protein sequences. . SAS is a tool which aims to bridge the gap between protein sequence and structural analysis, and aid identification of a protein sequence, by using structural information to recognize distant homologues.
SOSUI A useful tool for secondary structure prediction of membrane proteins from a protein sequence. The basic idea of prediction in this system is based on the physicochemical properties of amino acid sequences such as hydrophobicity and charges. The system deals with three types of prediction: discrimination of membrane proteins from soluble one, prediction of existence of transmembrane helices and determination of transmembrane helical regions.
Swiss-Model A fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide.
Sstructview: Rna Secondary Structure Java Applet A reusable interface based on the standard two-dimensional (2D) layout of RNA secondary structure.
Structural Analysis Tools at EBI Provides access to various services explicitly designed to help determination of a protein's 2D/3D structure. Offered by EMBL-European Bioinformatics Institute.
THE MEME SYSTEM Discover motifs in groups of related DNA or protein sequences using MEME and search sequence databases using motifs using MAST.
Tmap The TMAP program predicts transmembrane segments in proteins.
tmRDB Studies the structures and functions of the tmRNA The tmRDB provides aligned, annotated and phylogenetically ordered tmRNA sequences. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Where possible, direct links to primary sources are established.
TSEG: Prediction Tool for Transmembrane Segment in Proteins TSEG is based on a classification of transmembrane(TM) segments. TM segments in SWISS-PROT database are first divided into subgroups by the number of TM segments in proteins and the order it spans the membrane.
uRNA Database A tool to study the structures and functions of various uRNAs, providing aligned, annotated and phylogenetically ordered sequences. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Where possible, there are direct links to GenBank via the accession number.
VAST: Vector Alignment Search Tool Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the domains in MMDB is compared to every other one.

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