The Human Metabolome Database (HMDB) is a freely available database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. HMDB contains over 7900 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Additionally, approximately 7200 protein (and DNA) sequences are linked to these metabolite entries.

The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4800 drug entries including >1,350 FDA-approved small molecule drugs, 123 FDA-approved biotech (protein/peptide) drugs, 71 nutraceuticals and >3,243 experimental drugs. Additionally, more than 2,500 non-redundant protein (i.e. drug target) sequences are linked to these FDA approved drug entries. Each DrugCard entry contains more than 100 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.

The Protein Property Prediction and Testing Database (PPT-DB) is a collection of protein property databases for over 20 different protein properties including secondary structure, trans-membrane helices and beta barrels, accessible surface area, signal peptides, and more.

FooDB is a database on food constituents, chemistry and biology that has been under development since 2009. It currently has data on 28,500 food compounds and food associations. It is being jointly developed with Dr. Augustin Scalbert (IARC, Lyon). When completed in late 2012 or early 2013 it will be the most comprehensive resource on food composition in the world. It will provide information on both macronutrients and micronutrients, including many of the constituents that give foods their flavor, color, taste, texture and aroma. The link provided here gives some sample pages from the database.

The Toxin and Toxin Target Database (T3DB) is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. The database currently houses over 2900 toxins described by over 34 200 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to over 1300 corresponding toxin target records. Altogether there are over 33 800 toxin, toxin target associations.

The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing nearly 450 small molecule pathways found in humans. These include standard metabolic pathways (90), disease pathways (116), drug pathways (223) and metabolic signaling pathways (13). More than 70% of the pathways in SMPDB are found in no other pathway database (not even KEGG or HumanCyc). SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology.

The CSF Metabolome database is a freely available electronic database containing detailed information about 468 small molecule metabolites found in human CSF along with 1650 concentration values. The data tables may be sorted and searched by concentration values and ranges. The information includes literature and experimentally derived chemical data, clinical data and molecular/biochemistry data.

The Serum Metabolome database is a freely available electronic database containing detailed information about 4651 small molecule metabolites found in human serum along with 10895 concentration values. The data tables may be sorted and searched by concentration values and ranges. The information includes literature and experimentally derived chemical data, clinical data and molecular/biochemistry data.

The CyberCell Database (CCDB) is a comprehensive, web-accessible database designed to support and coordinate international efforts in modeling an Escherichia coli cell on a computer. The CCDB brings together both observed and derived quantitative data from numerous independent sources covering many aspects of the genomic, proteomic and metabolomic character of E.coli (strain K12).

The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae(also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases. YMDB contains metabolites arising from normal S. cerevisiae metabolism under defined laboratory conditions as well as metabolites generated by S. cerevisiae when used in baking and in the production of wines, beers and spirits. YMDB currently contains 2010 small molecules with 857 associated enzymes and 138 associated transporters.

The Bovine Metabolome Database (BMDB) The Bovine Metabolome Database (BMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in beef and dairy cattle. The information includes literature and experimentally derived information on bovine meat, bovine serum, bovine milk, bovine urine and bovine ruminal fluid.

E. coli Metabolome Database (ECMDB) is a freely available eletronic database containing detailed information about the >1620 metabolites found in E. coli (strain K12, MG1655). The information includes literature and experimentally derived information on the chemical data, spectral data and the molecular/biochemistry data.

MarkerDB will be a freely available resource that attempts to consolidate information on all known clinical biomarkers into a single source. Multiple types of markers are covered including metabolite based, genetic based, protein based and cell based markers.

Web Servers

PepMake generates a PDB coordinate file for polypeptide backbones using only the sequence and backbone dihedral angles as input.

VADAR (Volume, Area, Dihedral Angle Reporter) is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data.

MetaboAnalyst MetaboAnalyst is a comprehensive, Web-based tool designed for processing, analyzing, and interpreting metabolomic data. It handles most of the common metabolomic data types including compound concentration lists, spectral bin lists, peak lists, and raw MS spectra.

MetATT is a easy-to-use, web-based tool designed for time-series and two-factor metabolomics data analysis. MetATT offers a number of complementary approaches including 3D interactive principal component analysis, two-way heatmap visualization, two-way ANOVA, ANOVA-simultaneous component analysis and multivariate empirical Bayes time-series analysis.

MetPA (Metabolomics Pathway Analysis) is a free and easy-to-use web application designed to perform pathway analysis and visualization of quantitative metabolomic data.

MSEA is a web-based tool to help identify and interpret patterns of metabolite concentration changes in a biologically meaningful context for human and mammalian metabolomic studies.

MetaboMiner is a tool which can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D NMR spectra. MetaboMiner is able to handle both 1H-1H total correlation spectroscopy (TOCSY) and 1H-13C heteronuclear single quantum correlation (HSQC) data. It identifies compounds by comparing 2D spectral patterns in the NMR spectrum of the biofluid mixture with specially constructed libraries containing reference spectra of approximately 500 pure compounds.

PolySearch supports >50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is 'Given X, find all Y's' where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites.

Receiver Operating Characteristic (ROC) curves are generally considered the method of choice for evaluating the performance of potential biomarkers. ROCCET is a freely available web-based tool designed to assist clinicians and bench biologists in performing common ROC based analyses on their metabolomic data using both classical univariate and more recently developed multivariate approaches.

User-friendly, web-based analytical pipeline for comparative metagenomic studies. Input can be derived from either 16S rRNA data or NextGen shotgun sequencing.

Proteus is a high-performing integrated web server and a stand-alone application three high-performing de novo structure prediction methods (PSIPRED, JNET and TRANSSEC [a locally developed predictor]), a jury-of-experts consensus tool and a robust PDB-based structure alignment process to generate all of its secondary structure predictions. For water-soluble protein Proteus is able to achieve a very high level of accuracy (Q3=88%, SOV=90%). In the rare situation (20-30%) where a query protein shows no similarity whatsoever to any known structure, PROTEUS is still able to achieve a Q3 score of 79%. Proteus is not restricted to generating accurate secondary structures for water-soluble proteins, as it appears to perform well for integral membrane proteins (both helix-containing proteins and beta-sheet containing porins) that have remote homologues or a portion of a homologue in the PDB.

PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane β-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline.

BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences.

An interactive visual database containing all publicly available bacterial genomes. A fully labeled and zoomable genome map is provided for each genome. Sequence and text queries can be used to identify genes of interest, or maps can be navigated using a simple interface. BacMap is designed to serve as an intuitive and convenient tool for identifying orthologues and paralogues, studying operon conservation, and determining gene function.

ResProx (Resolution-by-proxy or Res(p)) is a web server that predicts the atomic resolution of NMR protein structures using only PDB coordinate data as input. More specfically, ResProx uses machine learning techniques to accurately estimate (with a correlation coefficient of 0.92 between observed and calculated) the atomic resolution of a protein structure from 25 measurable features that can be derived from its atomic coordinates. Because atomic resolution is a simple and near-universal measure of structure quality (i.e. < 2.0 Å is good, > 4.0 Å is bad), ResProx offers X-ray crystallographers and NMR spectroscopists the opportunity to easily assess the accuracy and quality of their 3D protein structures. It also allows them to assess whether their refinement methods have made their structures better (or worse) than what the experimental data suggests. Furthermore, since coordinate data is common to both X-ray and NMR, ResProx should allow structural biologists to use a single, easily understood number to compare the structures determined by NMR with those determined by X-ray crystallography.

CS23D 2.0 is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input. Unlike conventional NMR methods, which require NOE and/or J-coupling data, CS23D2.0 uses only chemical shift information to generate a 3D structure of the protein of interest. CS23D2.0 accepts chemical shift files in either SHIFTY or BMRB formats and produces a set of PDB coordinates for the protein in about 10-15 minutes. CS23D2.0 uses a combination of maximal subfragment assembly, chemical shift threading, shift-based torsion angle prediction and chemical shift refinement to generate and refine the protein coordinates. Tests indicate that CS23D2.0 converges (i.e. finds a solution) for about 90% of protein queries. The performance is dependent on the completeness of the chemical shift assignments and the similarity of the query protein to known 3D folds.

SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input. SHIFTX2 combines ensemble machine learning methods with sequence alignment-based methods to calculate protein chemical shifts for backbone and side chain atoms.

The Re-referenced Protein Chemical shift Database (RefDB) is a database of carefully corrected or re-referenced chemical shifts, derived from the BioMagRes Bank. The process involves predicting protein 1H, 13C and 15N chemical shifts using X-ray or NMR coordinate data via SHIFTX and then comparing those predictions to the observed shifts reported in the BMRB (via SHIFTCOR). RefDB provides a standard chemical shift resource for NMR spectroscopists, wishing to derive or compute chemical shift trends in peptides and proteins.

PHAST(PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage “cornerstone” feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage “quality” and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views.Furthermore, tests indicate that PHAST is as accurate or slightly more accurate than all available phage finding tools, with sensitivity of 85.4% and positive predictive value of 94.2%.

Proteome Analyst (PA) is an online tool used by researchers to rapidly analyze proteins. Using machine learning technologies, PA can accurately predict the subcellular localization and high level function of user submitted proteins.

Users can also analyze proteins using common bioinformatics tools such as: BLAST, HMMer, PROSITE, and PSIPRED.

Standalone Programs/Applications

PANAV is a Java based structure-independent chemical shift validation and re-referencing tool. It is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches.

A standalone version is also available. Download here.

Version 2 of the standalone version is now available. Download here.

Legacy Applications (Unmaintained)

SuperPose is a protein superposition server. SuperPose calculates protein superpositions using a modified quaternion approach. From a superposition of two or more structures, SuperPose generates sequence alignments, structure alignments, PDB coordinates, RMSD statistics, Difference Distance Plots, and interactive images of the superimposed structures. The SuperPose web server supports the submission of either PDB-formatted files or PDB accession numbers.

MovieMaker is a web server that allows short (~10 sec), downloadable movies to be generated of protein dynamics. It accepts PDB files or PDB accession numbers as input and automatically outputs colorful animations covering a wide range of protein motions and other dynamic processes. Users have the option of animating 1) simple rotation 2) morphing between two end conformers 3) short-scale, picosecond vibrations; 4) ligand docking; 5) protein oligomerization; 6) mid-scale nanosecond (ensemble) motions; and 7) protein folding/unfolding. Note: MovieMaker is not a molecular dynamics server and does not perform MD calculations.

GelScape is a web-based gel viewing and annotation system.

With Shifty you can predict 1H, 13C, and 15N chemical shifts for your favourite protein using only its amino acid sequence as input. The technique uses dynamic programming to detect sequence homologies between your query and sequences of hundreds of previously assigned protiens in the BioMagResBank.

Shiftcor compares, identifies, corrects and re-referencs 1H, 13C and 15N backbone chemical shifts of peptides and proteins by comparing the observed chemical shifts with the predicted chemical shifts derived from the 3D structure (PDB corrdinates) of the protein(s)of interest.

SHIFTOR is a program for predicting φ, ψ, χ1, and ω torsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology. For a test set of 31 proteins, SHIFTOR 30o-accuracy of predicting φ and ψ is close to 90%. The average χ1 accuracy is 81% while the ω accuracy is 99.98% for trans peptide bond identification and 93% for cis peptide bond identification. Overall, the program is 100X faster and its predictions are approximately 30% better than existing methods.

Thrifty use threading method etc. to predict protein 3D structures from chemical shifts.

A web server that rapidly generates 3D protein structures (PDB coordinates) from their corresponding protein sequence.

RCI webserver predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts (Cα, CO, Cβ, N, Hα, NH) and estimating values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index.

PREDITOR is a program for PREDIcting φ, ψ, χ1, and ω TORsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology. PREDITOR 30o-accuracy of predicting φ and ψ is close to 90%. The average χ1 accuracy is 84% while the ω accuracy is 99.98% for trans peptide bond identification and 93% for cis peptide bond identification. Overall, the program is 35X faster and its predictions are approximately 20% better than existing methods.

SimCell is a DCA Cell simulator used to simulate cellular and biochemical processes.The user, through the use of the SimCell Interface may create: small molecules, membrane, membrane proteins, protein/RNA molecules, DNA molecules and Genes. These cellular components can then interact amongst themselves to create fascinating new processes.

A user friendly program for calculating coupling constants from TOCSY, NOESY, HMQC traces.