Proteomics and peptidomics analysis of Sepiae Endoconcha / 中国中药杂志

Shotgun based proteomics and peptidomics analysis were used to investigate the proteins and peptides in marine traditional Chinese medicine(TCM) Sepiae Endoconcha(cuttlebone). Peptides were extracted from cuttlebone by acidified methanol, and then strong cation exchange(SCX) resin was used to enrich those peptides. Also, proteins from cuttlebone were extracted and digested by trypsin. nano-LC Q Exactive Orbitrap mass spectrometry was used to analyze proteins and peptides from cuttlebone. As a result, a total of 16 proteins and 168 peptides were identified by protein database search, and 328 peptides were identified by De novo sequencing. The identified proteins were hemocyanin, enolase, myosin, actin, calmodulin, etc., and the identified peptides were derived from actin, histone, and tubulin. All these proteins and peptides were important components in cuttlebone, which would provide important theoretical and research basis for marine TCM cuttlebone investigations.

In silico analysis of putative drug and vaccine targets of the metabolic pathways of Actinobacillus pleuropneumoniae using a subtractive/comparative genomics approach

Actinobacillus pleuropneumoniae is a Gram-negative bacterium that resides in the respiratory tract of pigs and causes porcine respiratory disease complex, which leads to significant losses in the pig industry worldwide. The incidence of drug resistance in this bacterium is increasing; thus, identifying new protein/gene targets for drug and vaccine development is critical. In this study, we used an in silico approach, utilizing several databases including the Kyoto Encyclopedia of Genes and Genomes (KEGG), the Database of Essential Genes (DEG), DrugBank, and Swiss-Prot to identify non-homologous essential genes and prioritize these proteins for their druggability. The results showed 20 metabolic pathways that were unique and contained 273 non-homologous proteins, of which 122 were essential. Of the 122 essential proteins, there were 95 cytoplasmic proteins and 11 transmembrane proteins, which are potentially suitable for drug and vaccine targets, respectively. Among these, 25 had at least one hit in DrugBank, and three had similarity to metabolic proteins from Mycoplasma hyopneumoniae, another pathogen causing porcine respiratory disease complex; thus, they could serve as common therapeutic targets. In conclusion, we identified glyoxylate and dicarboxylate pathways as potential targets for antimicrobial therapy and tetra-acyldisaccharide 4′-kinase and 3-deoxy-D-manno-octulosonic-acid transferase as vaccine candidates against A. pleuropneumoniae.

PTMD: A Database of Human Disease-associated Post-translational Modifications / 基因组蛋白质组与生物信息学报·英文版

Various posttranslational modifications (PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM-disease associations (PDAs) would be a great help for both academic research and clinical use. In this work, we reported PTMD, a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of disease-associated PTM events. By reconstructing a disease-gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http://ptmd.biocuckoo.org.

Network pharmacology study of Xiaoxuming Decoction based on vasodilatory and vasoconstrictory related GPCR targets / 中国中药杂志

In this study, bioinformatics methods such as molecular docking and network pharmacology were adopted to establish Xiaoxuming Decoction (XXMD) "compound-vasodilatory and vasoconstrictory related G protein-coupled receptors (GPCR) targets" network, then the vascular function regulatory effective components and the potential targets of XXMD were analyzed. Based on the XXMD herb sources, the chemical structures of the compounds were retrieved from the national scientific data sharing platform for population and health pharmaceutical information center, TCMSP database and the latest research literatures. The chemical molecular library was established after class prediction and screening for medicinal and metabolic properties. Then, five kinds of vasodilatory and vasoconstrictory related GPCR crystal structure including 5-HT receptors (5-HT1AR, 5-HT1BR), AT1R, β2-AR, hUTR and ETB were retrieved from RCSB Protein Data Bank database or constructed by homology modeling of Discovery Studio 4.1 built-in modeling tools. After virtual screening by Libdock molecular docking, the highest rated 50 compounds of each target were collected and analyzed. The collected data were further used to construct and analyze the network by Cytoscape 3.4.0. The results showed that most of the chemical composition effects were associated with different vasodilatory and vasoconstrictory related GPCR targets, while a few effective components could be applied to multiple GPCR targets at the same time, therefore forming synergies and vasorelaxant effects of XXMD.

Quaternion-based Characterization of Protein α Helix / 生物医学工程学杂志

This paper proposes a method based on quaternion for characterization a helix of proteins. The method defines the parameter called Quaternion Helix Axis Spherical Distance (QHASD) on the basis of mapping protein Cα frames' helical axis onto a unit sphere, and uses QHASD to characterize the a helix of the protein secondary structure. Application of this method has been verified based on the PDBselect database, with an a helix characterization accuracy of 91.7%. This method possesses significant advantages of high detection accuracy, low computation and clear geometric significance.

Specific alterations in plasma proteins during depressed, manic, and euthymic states of bipolar disorder

Bipolar disorder (BD) is a common psychiatric mood disorder affecting more than 1-2% of the general population of different European countries. Unfortunately, there is no objective laboratory-based test to aid BD diagnosis or monitor its progression, and little is known about the molecular basis of BD. Here, we performed a comparative proteomic study to identify differentially expressed plasma proteins in various BD mood states (depressed BD, manic BD, and euthymic BD) relative to healthy controls. A total of 10 euthymic BD, 20 depressed BD, 15 manic BD, and 20 demographically matched healthy control subjects were recruited. Seven high-abundance proteins were immunodepleted in plasma samples from the 4 experimental groups, which were then subjected to proteome-wide expression profiling by two-dimensional electrophoresis and matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight tandem mass spectrometry. Proteomic results were validated by immunoblotting and bioinformatically analyzed using MetaCore. From a total of 32 proteins identified with 1.5-fold changes in expression compared with healthy controls, 16 proteins were perturbed in BD independent of mood state, while 16 proteins were specifically associated with particular BD mood states. Two mood-independent differential proteins, apolipoprotein (Apo) A1 and Apo L1, suggest that BD pathophysiology may be associated with early perturbations in lipid metabolism. Moreover, down-regulation of one mood-dependent protein, carbonic anhydrase 1 (CA-1), suggests it may be involved in the pathophysiology of depressive episodes in BD. Thus, BD pathophysiology may be associated with early perturbations in lipid metabolism that are independent of mood state, while CA-1 may be involved in the pathophysiology of depressive episodes.

Perioperative morbidity and mortality in the first year of life: a systematic review (1997-2012) / Morbimortalidade perioperatória no primeiro ano de idade: revisão sistemática (1997-2012)

ABSTRACTBACKGROUND AND OBJECTIVES: Although many recognize that the first year of life and specifically the neonatal period are associated with increased risk of anesthetic morbidity and mortality, there are no studies directed to these pediatric subpopulations. This systematic review of the scientific literature including the last 15 years aimed to analyze the epidemiology of morbidity and mortality associated with general anesthesia and surgery in the first year of life and particularly in the neonatal (first month) period.CONTENT: The review was conducted by searching publications in Medline/PubMed databases, and the following outcomes were evaluated: early mortality in the first year of life (<1 year) and in subgroups of different vulnerability in this age group (0-30 days and 1-12 months) and the prevalence of cardiac arrest and perioperative critical/adverse events of various types in the same subgroups.CONCLUSIONS: The current literature indicates great variability in mortality and morbidity in the age group under consideration and in its subgroups. However, despite the obvious methodological heterogeneity and absence of specific studies, epidemiological profiles of morbidity and mortality related to anesthesia in children in the first year of life show higher frequency of morbidity and mortality in this age group, with the highest peaks of incidence in the neonates' anesthesia.

RESUMOJUSTIFICATIVA E OBJETIVOS: Embora muitos reconheçam que a idade inferior a um ano e especificamente o período neonatal estejam associados a maior risco de morbimortalidade anestésica, não existem estudos dirigidos a essas subpopulações pediátricas. Esta revisão sistemática das publicações científicas dos últimos 15 anos teve como objetivo analisar o perfil epidemiológico da morbimortalidade relacionada com a anestesia geral e cirurgia no primeiro ano de idade e em particular no período neonatal (primeiro mês de idade).CONTEúDO: A revisão foi conduzida por pesquisa de publicações nas bases de dados Medline/PubMed. Foram avaliados os seguintes desfechos: mortalidade precoce no primeiro ano de idade (< 1A) e em subgrupos de diferente vulnerabilidade nesta faixa etária (0-30 dias e 1-12 meses) e prevalência de parada cardíaca e eventos críticos/adversos perioperatórios de diversos tipos nos mesmos subgrupos.CONCLUSÕES: A literatura corrente indica grande variabilidade nos índices de mortalidade e morbidade na faixa etária em análise, bem como nos seus subgrupos. No entanto, apesar da óbvia heterogeneidade metodológica e da ausência de estudos específicos, os perfis epidemiológicos de morbimortalidade relacionada com a anestesia de crianças no primeiro ano de idade mostram frequência mais alta de morbimortalidade nessa faixa etária, com os maiores picos de incidência na anestesia de neonatos.

Proteomics analysis of tissue samples from patients with squamous cell carcinoma of the penis and positive to human papillomavirus

ABSTRACTPurpose:The aim of this study was to identify possible protein biomarkers and/or candidates for therapeutic targets in tissues of patients with SCCP, infected by HPV, applying one dimensional electrophoresis (1DE), followed by direct mass spectrometry (MS) analysis.Materials and Methods:Tissues from 10 HPV positive patients with SCCP and from 10 patients with HPV negative non-tumorous penile foreskins were analyzed applying 1D electrophoresis, followed by analysis with direct mass spectrometry (MS).Results:Sixty-three different proteins were identified in the first group and 50 in the second group. Recognition was possible for 28 proteins exclusively detected in Group 1 and 21 proteins presented only in Group 2.Conclusion:Some proteins in the first group are directly involved in the development of other types of cancer, and therefore, suitable for analysis. Complement C3 protein is a strong candidate for evaluating SCCP patients.

Molecular docking analysis of xanthine oxidase inhibition by constituents of cichory / 中国中药杂志

Human xanthine oxidase is considered to be a target for therapy of hyperuricemia. Cichorium intybus is a Chinese plant medicine which widely used in Xinjiang against various diseases. In order to screen the inhibitors of xanthine oxidase from C. intybus and to explore main pharmacological actions of cichory a compound collection of C. intybus was built via consulting related references about chemical research on cichory. The three-dimensional crystal structure of xanthine oxidase (PDB code: 1N5X) from Protein Data Bank was downloaded.. Autodock 4.2 was employed to screen the inhibitors of xanthine oxidase from cichory 70 compounds were found to possess quite low binding free energy comparing with TEI (febuxostat). C. intybus contains constituents possessing potential inhibitive activity against xanthine oxidase. It can explain the main pharmacological actions of cichory which can significantly lower the level of serum uric acid.

In-silico analysis of heat shock protein 47 for identifying the novel therapeutic agents in the management of oral submucous fibrosis.

Background: Heat shock proteins-47 (HSP47) is a collagen specific molecular chaperone, involved in the processing and/or secretion of procollagen. It seems to be regularly upregulated in various fibrotic or collagen disorders. Hence, this protein can be a potential target for the treatment of various fibrotic diseases including oral submucous fibrosis (OSF), which is a collagen metabolic disorder of oral cavity and whose etiopathogeneic mechanism and therapeutic protocols are still not well documented. Aim: The aim of this study is to identify the novel therapeutic agents using in-silico methods for the management of OSF. Objectives: The objectives of this study are to identify the binding sites of HSP47 on the collagen molecule and to identify the lead compound with anti-HSP47 activity from the library of natural compounds, using in-silico methodology. Materials and Methods: The web-based and tool based in-silico analysis of the HSP47 and collagen molecules are used in this study. The crystal structure of collagen and HSP47 were retrieved from Protein Data Bank website. The binding site identification and the docking studies are done using Molegro Virtual Docker offline tool. Results: Out of the 104 Natural compounds, six ligands are found to possess best binding affinity to the binding amino acid residues. Silymarin binds with the 4AU2A receptor and the energy value are found to be −178.193 with four Hbonds. The other best five natural compounds are hesperidin, ginkgolides, withanolides, resveratrol, and gingerol. Our findings provide the basis for the in-vitro validation of the above specified compounds, which can possibly act as "lead" molecules in designing the drugs for OSF. Conclusion: HSP47 can be a potential candidate to target, in order to control the production of abundance collagen in OSF. Hence, the binding sites of HSP47 with collagen are identified and some natural compounds with a potential to bind with these binding receptors are also recognized. These natural compounds might act as anti-HSP47 lead molecules in designing novel therapeutic agents for OSF, which are so far unavailable.

Applications of complementarity plot in error detection and structure validation of proteins.

The complementarity plot (CP) is based on packing and electrostatics of amino acid residues buried within globular proteins and is a sensitive indicator of the harmony or disharmony of interior residues with regard to short and long range forces sustaining the native fold. As a structure validation tool, it has already been reported to be effective in detecting erroneous side-chain torsions in obsoleted structures. The current study describes the design of several local and global scores based on CP and surveys their utilities in discriminating between obsolete structures and their corresponding upgraded counterparts, detection of wrong rotamer assignments and in identifying packing anomalies. CPs are especially effective in the detection of low-intensity errors (in main-chain geometrical parameters) diffused over the entire polypeptide chain. The methodology is also used to confirm the integral role played by strategic deviations (in main-chain geometrical parameters) in maintaining fold integrity, as reversal to their corresponding ideal values (either unimodal or conformation dependent) lead to large-scale structural distortions. A special feature of this validation tool is to signal unbalanced partial charges within protein interiors. The application of CP in protein homology modeling and protein design is also demonstrated.

Comparative proteomic analysis of different developmental stages of the edible mushroom Termitomyces heimii

BACKGROUND: Termitomyces heimii is a basidiomycete fungus that has a symbiotic relationship with termites, and it is an edible mushroom with a unique flavour and texture. T. heimii is also one of the most difficult mushrooms to cultivate throughout the world. Little is known about the growth and development of these mushrooms, and the available information is insufficient or poor. The purpose of this study was to provide a base of knowledge regarding the biological processes involved in the development of T. heimii. The proteomic method of 2 dimensional difference gel electrophoresis 2D-DIGE was used to determine and examine the protein profiles of each developmental stage (mycelium, primordium and fruiting body). Total proteins were extracted by TCA-acetone precipitation. RESULTS: A total of 271 protein spots were detected by electrophoresis covering pH 3 - 10 and 10 - 250 kDa. Selected protein spots were subjected to mass spectrometric analyses with matrix-assisted laser desorption/ionisation (MALDI TOF/TOF). Nineteen protein spots were identified based on peptide mass fingerprinting by matching peptide fragments to the NCBI non-redundant database using MASCOT software. The 19 protein spots were categorised into four major groups through KEGG pathway analysis, as follows: carbohydrate metabolism, energy metabolism, amino acid metabolism and response to environmental stress. CONCLUSIONS: The results from our study show that there is a clear correlation between the changes in protein expression that occur during different developmental stages. Enzymes related to cell wall synthesis were most highly expressed during fruiting body formation compared to the mycelium and primordial stages. Moreover, enzymes involved in cell wall component degradation were up-regulated in the earlier stages of mushroom development.

SFannotation: A Simple and Fast Protein Function Annotation System

Owing to the generation of vast amounts of sequencing data by using cost-effective, high-throughput sequencing technologies with improved computational approaches, many putative proteins have been discovered after assembly and structural annotation. Putative proteins are typically annotated using a functional annotation system that uses extant databases, but the expansive size of these databases often causes a bottleneck for rapid functional annotation. We developed SFannotation, a simple and fast functional annotation system that rapidly annotates putative proteins against four extant databases, Swiss-Prot, TIGRFAMs, Pfam, and the non-redundant sequence database, by using a best-hit approach with BLASTP and HMMSEARCH.

Priorização de alvos para fármacos no combate a doenças tropicais negligenciadas causadas por protozoários / Prioritization of targets for drugs to fight neglected tropical diseases caused by protozoan

As doenças negligenciadas são doenças infecciosas que afetam principalmente a população mais pobre do mundo. Os fármacos existentes para o combate a essas doenças causam muitos efeitos colaterais aos pacientes e não são suficientes ou são inacessíveis à eles. Além disso, ainda há a resistência aos fármacos. Neste sentido, identificar alvos para a descoberta de novos fármacos se faz necessário. Este trabalho propõe uma metodologia para apoiar a priorização de alvos no combate a doenças tropicais negligenciadas causadas por cinco protozoários: Entamoeba histolytica, Leishmania major, Plasmodium falciparum, Trypanosoma brucei e T. cruzi, baseando-se nos conceitos de essencialidade e drogabilidade da proteína. A metodologia aproveita-se da vasta quantidade de dados e informações disponíveis publicamente em bases de dados genômicas, bioquímicas e farmacológicas, além da literatura biomédica, para buscar e integrar dados e informações de organismos modelo e proteínas alvo de fármaco para sugerir candidatos (proteínas alvo) essenciais e drogáveis para os protozoários, levantando assim, possíveis alvos para posteriores estudos e experimentosPara a obtenção destes dados foi utilizada a abordagem de anotação semântica baseada em ontologia para extrair dados a partir de artigos científicos e os conceitos de homologia e ortologia entre sequências de proteínas armazenadas em bases de dados semi-estruturadas de modo a levantar candidatos essenciais e drogáveis. Exemplos dos resultados gerados são mostrados, assim como algumas relações encontradas, e possíveis integrações entre os dados extraídos da literatura e dos resultados de homologia e ortologia...

Neglected diseases are infectious diseases that primarily affect the poorest people inthe world. The existing drugs to fight these diseases cause many side effects topatients and are not sufficient or inaccessible. Another problem is that there still isdrug resistance. Accordingly, it is very important to identify targets for new drugs.This study proposes a methodology to support the prioritization of targets to combatneglected tropical diseases caused by five protozoan Entamoeba histolytica,Leishmania Major, Plasmodium falciparum, Trypanosoma cruzi and T. brucei, basedon the concepts of protein essentiality and druggability. The methodology takesadvantage of the large amount of data and information publicly available on genomic,biochemical and pharmacological databases, and also the biomedical literature to seekand integrate data and information from model organisms and drug target proteins tosuggest essential and druggable candidates (target proteins) for protozoa, raising thepossibility of targets for future studies and experiments. To obtain these data we usedthe approach of ontology-based semantic annotation to extract data from scientificarticles and the concepts of homology and orthology between protein sequencesstored in semi-structured databases, in order to raise essential and drugablecandidates. Examples of the results generated are shown, as well as somerelationships found, and possible integration between the data extracted from theliterature and the results of homology and orthology...

Dynamic protein-protein interaction subnetworks of lung cancer in cases with smoking history / 癌症

Smoking is the primary cause of lung cancer and is linked to 85% of lung cancer cases. However, how lung cancer develops in patients with smoking history remains unclear. Systems approaches that combine human protein-protein interaction (PPI) networks and gene expression data are superior to traditional methods. We performed these systems to determine the role that smoking plays in lung cancer development and used the support vector machine (SVM) model to predict PPIs. By defining expression variance (EV), we found 520 dynamic proteins (EV>0.4) using data from the Human Protein Reference Database and Gene Expression Omnibus Database, and built 7 dynamic PPI subnetworks of lung cancer in patients with smoking history. We also determined the primary functions of each subnetwork: signal transduction, apoptosis, and cell migration and adhesion for subnetwork A; cell-sustained angiogenesis for subnetwork B; apoptosis for subnetwork C; and, finally, signal transduction and cell replication and proliferation for subnetworks D-G. The probability distribution of the degree of dynamic protein and static protein differed, clearly showing that the dynamic proteins were not the core proteins which widely connected with their neighbor proteins. There were high correlations among the dynamic proteins, suggesting that the dynamic proteins tend to form specific dynamic modules. We also found that the dynamic proteins were only correlated with the expression of selected proteins but not all neighbor proteins when cancer occurred.

Protein Backbone Torsion Angle-Based Structure Comparison and Secondary Structure Database Web Server

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.

Identificación bacteriana basada en el espectro de masas de proteínas: Una nueva mirada a la microbiología del siglo XXI / Bacterial identification based on protein mass spectrometry: A new insight at the microbiology of the 21st century

Bacterial identification is important for the proper treatment of infected patients hospitalized with serious infections especially in critical care units. Identification by conventional methods used in microbiology laboratories takes at least 16 hours since a culture is positive. The introduction of mass spectrometry, specifically MALDI-TOF MS (matrix-assisted laser desorption/ ionization time-of-flight mass spectrometer) in the microbiology laboratory could mean a radical change in the identification accuracy, turn around time (6 minutes per bacteria) and cost (about 5 times cheaper than conventional identification). Since its introduction in clinical microbiology laboratories in 2008, many reports about its usefulness in identifying microorganisms from colonies, as well as directly from positive blood cultures and urine samples have been published. This review describes MALDI-TOF MS methodology, its identification performance for bacteria (aerobic and anaerobic), mycobacterium and yeasts, its future applications in microbiology and its main disadvantages.

La identificación bacteriana es muy importante en el manejo adecuado de los pacientes infectados, especialmente aquellos con infecciones graves hospitalizados en unidades de pacientes críticos. La identificación por los métodos convencionales utilizados en los laboratorios de microbiología clínica demora al menos 16 horas desde que un cultivo es positivo. La introducción de la espectrometría de masas, específicamente del espectrómetro de masas por tiempo de migración (tiempo de vuelo) con desorción/ionización laser asistida por una matriz (MALDI-TOF MS, por su sigla en inglés matrix-assisted laser desorption/ionization time-of-flight mass spectrometer), en el laboratorio de microbiología podría significar un cambio radical en la precisión de la identificación, el tiempo de detección (6 minutos por bacterias) y el costo (aproximadamente 5 veces más económico que la identificación convencional). Desde su introducción en los laboratorios de microbiología clínica en el año 2008, se han escrito numerosas publicaciones sobre su utilidad en la identificación de microorganismos desde colonias, así como directamente desde hemocultivos positivos y de muestras de orina. Esta revisión describe la metodología de MALDI-TOF MS, su rendimiento en la identificación de bacterias aerobias, anaerobias, micobacterias y levaduras, sus futuras aplicaciones en microbiología y sus principales desventajas.

Bioinformatics advances in saliva diagnostics / 国际口腔科学杂志·英文版

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval,integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart.

Network-based local and global consistency of cardiovascular genes / 中国中药杂志

Drug targets discovery is one of the most important elements in new drug development, and a variety of methods have been developed recently from this point of view. This paper proposed a network-based local and global consistency for cardiovascular genes identification. Results were evaluated through the widely used database HPRD and DrugBank. Results showed that our algorithm can give reasonable candidate targets set. The method in this paper could be an impressive solution for targets searching.

SNObase, a database for S-nitrosation modification

S-Nitros(yl)ation is a ubiquitous redox-based post-translational modification of protein cysteine thiols by nitric oxide or its derivatives, which transduces the bioactivity of nitric oxide (NO) by regulation of protein conformation, activity, stability, localization and protein-protein interactions. These years, more and more S-nitrosated proteins were identified in physiological and pathological processes and the number is still growing. Here we developed a database named SNObase ( http://www.nitrosation.org ), which collected S-nitrosation targets extracted from literatures up to June 1st, 2012. SNObase contained 2561 instances, and provided information about S-nitrosation targets, sites, biological model, related diseases, trends of S-nitrosation level and effects of S-nitrosation on protein function. With SNObase, we did functional analysis for all the SNO targets: In the gene ontology (GO) biological process category, some processes were discovered to be related to S-nitrosation ("response to drug", "regulation of cell motion") besides the previously reported related processes. In the GO cellular component category, cytosol and mitochondrion were both enriched. From the KEGG pathway enrichment results, we found SNO targets were enriched in different diseases, which suggests possible significant roles of S-nitrosation in the progress of these diseases. This SNObase means to be a database with precise, comprehensive and easily accessible information, an environment to help researchers integrate data with comparison and relevancy analysis between different groups or works, and also an SNO knowledgebase offering feasibility for systemic and global analysis of S-nitrosation in interdisciplinary studies.