Provides basics, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes. The database is expected to give impetus to further research on autophagy by providing basic and specialized data on the subject.
A reference for all scientists working on p53, including information on p53 structure and function, the description of all p53 monoclonal antibodies and the phylogenetic analysis of p53. More than 50% of human tumors carry TP53 gene mutations and in consequence more than 45,000 somatic and germline mutations have been gathered in the UMD TP53 database. Analyses of these mutations have been invaluable for bettering our knowledge on the structure-function relationships within the TP53 protein and the high degree of heterogeneity of the various TP53 mutants in human cancer.
Provides a data resource for autophagy researches. ARN collects up to 1480 proteins with more than 4000 of autophagy components in humans. It also contains more than 400 transcription factors (TF) and 380 miRNA that can serve to adjust autophagy components and their protein regulators including signaling pathways from the SignaLink 2 resource. Disease and cancer type annotations are available for each protein in this database.
Apoptosis is coordinated by members of the caspase family of aspartic acid-specific proteases. The CASBAH is a searchable web resource which contains information pertaining to all currently known caspase substrates.
A public repository containing information about the human genes described so far as involved in autophagy. HADb provides a complete and an up-to-date list of human genes and proteins involved directly or indirectly in autophagy as described in literature. General information, comments and genomic annotations had been used to describe genes. The display of annotations and the navigation on the genome is then possible by using an internal GBrowse or a link to Ensembl.
Deals with autophagy, necrosis and apoptosis orchestrators for eight organisms. THANATOS provides information related with proteins associated with autophagy manually curated from several taxonomies. This online resource contains more than 190 000 protein records and data about more than 160 eukaryotes investigated to look after possible orthologs. Searches can be made by processes, species, batch or BLAST search as well as by identifiers.
Compiles data about miRNAs and their targets in programmed cell death (PCD) network. miRDeathDB gathers over 200 entries dealing with more than 80 miRNAs and about 90 protein-coding genes in five species as well as links towards external genomic, proteomic and disease-associated data. Searches can be made by PCD-associated miRNAs and their targets based on gene principal symbols.
A database of proteins involved in cell death. DeathBase compiles relevant data on the function, structure and evolution of proteins involved in apoptosis and other forms of cell death in several organisms. Information contained in this database is subjected to manual curation. You can contribute to maintain the DeathBase by editing the wikipage for any protein.
A dedicated database of 82 apoptosis proteins. ApoCanD comprises of crucial information of apoptosis proteins in the context of cancer. Genomic status of proteins in the form of mutation, copy number variation and expression in thousands of tumour samples and cancer cell lines are the major bricks of this database. Availability of other information e.g. gene essentiality data, tertiary structure, sequence alignments, sequences profiles, post-translational modifications makes it even more useful for the researchers. ApoCanD provides plenty of opportunities for the researchers in exploring the role of apoptosis in cancer.
Comprehends data from apoptosis, autophagy, cytotoxic granule-mediated cell death, excitotoxicity, mitotic catastrophe, paraptosis, pyroptosis, and Wallerian degeneration. The CDP database represents a useful tool to consolidate data from proteome analyses of programmed cell death.
An extensively-curated database dedicated for researchers working on yeast apoptosis. It is an open platform established to facilitate the organization and sharing of knowledge. yApoptosis structurally collects annotated information of apoptotic genes such as pathway information, GO terms, relevant literature, and provides additional links to protein information, gene expression and interaction data.
Provides information about potential caspase cleavage sites in a verified set of human proteins involved in NDs. CaspNeuroD is a relational database of in silico predicted caspase cleavage sites in human proteins associated with NDs. This database could be used for identifying new caspase substrates and further our understanding of the caspase-mediated substrate cleavage in NDs. It provides also information about the conservation of cleavage positions in corresponding orthologs, and information about the positions of single nucleotide polymorphisms and posttranslational modifications (PTMs) that may modulate the caspase cleavage efficiency.
A collection of sequence, structural and functional information about BCL-2 homologous and BH3-containing proteins, which are among the most studied in cell biology. The Web interface allows for easy browsing of the site and fast access to data, as well as sequence analysis with generic and specific tools. BCL2DB provides a helpful and powerful tool to both 'BCL-2-ologists' and researchers working in the various fields of physiopathology.
Provides data for over 2400 genes involved directly or indirectly, in apoptotic pathways of more than 350 different organisms. AGIS is to provide the maximum available information for each gene/protein involved in apoptosis and to facilitate researchers in their quest for information directly or indirectly related to apoptotic signal transduction pathways. It aims to become a major resource in understanding the genetics of human apoptosis.
Presently, I am working as professor & head of Computational Biology, IIIT-Delhi. Before joining IIT Delhi, I worked as Scientist at Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh, India. More information is available from following sites Home Page of Gajendra P. S. Raghava's Group (http://www.imtech.res.in/raghava/) , Computational Resources for Drug Discovery (http://crdd.osdd.net/) , A Customized Operating System for Drug Discovery (http://osddlinux.osdd.net/)and and Gajendra Pal Singh Raghava - Wikipedia (https://en.wikipedia.org/wiki/Gajendra_Pal_Singh_Raghava) .
Dr. Yashwanth Subbannayya obtained his M.Sc. degree in Medical Biochemistry from Manipal University. He qualified the competitive CSIR-UGC National Eligibility Test and joined the Institute of Bioinformatics, Bangalore as a UGC Junior Research Fellow. As part of his Ph.D. work, he studied the molecular mechanisms of gastric cancer in clinical specimens using quantitative proteomic technologies. This study, the results of which were published in Cancer Biology and Therapy, yielded a novel therapeutic target for gastric cancer- CAMKK2. Further, he also studied the serum proteome of gastric cancer patients and developed assays for potential markers using the revolutionary multiple reaction monitoring approach. The results of this study were published in Journal of Proteomics. In addition to his research work, he also trained extensively in sample preparation for mass spectrometry, fractionation techniques and gained expertise in quantitative proteomic techniques and data analysis. In addition, he also trained extensively in various validation platforms including immunohistochemsitry, multiple reaction monitoring and Western blot. He has also worked as a curator for several biological databases including NetPath, Human Protein Reference Database (HPRD) and Breast cancer database. His work in various research projects have yielded him 23 publications either as lead author or co-author in peer reviewed journals. He is a reviewer for the journal Proteomics.
Dr. Yashwanth Subbannayya joined the YU-IOB Center for Systems Biology and Molecular Medicine in June, 2015. During the initial period, his job consisted of assisting other personnel of the university in the establishment of YU-IOB Center for Systems Biology and Molecular Medicine. He was also involved in training of Ph.D. students in biological aspects. After the establishment of the center, he trained in cell culture techniques and metabolomics analysis. At YU-IOB CSBMM, he is studying the molecular mechanisms in various cancers including oral cancer. In addition, he is studying the molecular mechanisms as well as the metabolic constituents of traditional medicine formulations using mass spectrometry technologies. In June 2016, he convened the national symposium “Genomics in clinical practice: Future of precision medicine” held at Yenepoya University on June 1 and 2, 2016. The resource persons included 16 individuals from various academic organizations as well as industry. The symposium was attended by 218 participants from 24 institutions around India. He is a member of the Scientific Review Board of Yenepoya Research Centre where he facilitates timely scientific review of research projects.