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Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for in silico analyses of biological queries using computational and statistical techniques.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models. The term structural has the same meaning as in structural biology, and structural bioinformatics can be seen as a part of computational structural biology. The main objective of structural bioinformatics is the creation of new methods of analysing and manipulating biological macromolecular data in order to solve problems in biology and generate new knowledge.
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland.
RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 1990s.
Institute for Systems Biology (ISB) is a non-profit research institution located in Seattle, Washington, United States. ISB concentrates on systems biology, the study of relationships and interactions between various parts of biological systems, and advocates an interdisciplinary approach to biological research.
The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.
Sir Thomas Leon Blundell, is a British biochemist, structural biologist, and science administrator. He was a member of the team of Dorothy Hodgkin that solved in 1969 the first structure of a protein hormone, insulin. Blundell has made contributions to the structural biology of polypeptide hormones, growth factors, receptor activation, signal transduction, and DNA double-strand break repair, subjects important in cancer, tuberculosis, and familial diseases. He has developed software for protein modelling and understanding the effects of mutations on protein function, leading to new approaches to structure-guided and Fragment-based lead discovery. In 1999 he co-founded the oncology company Astex Therapeutics, which has moved ten drugs into clinical trials. Blundell has played central roles in restructuring British research councils and, as President of the UK Science Council, in developing professionalism in the practice of science.
The Worldwide Protein Data Bank, wwPDB, is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.
The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located. As of 2015, the resource contained over 2,600 entries with a mean resolution of 15Å.
David S. Eisenberg is an American biochemist and biophysicist best known for his contributions to structural biology and computational molecular biology, a professor at the University of California, Los Angeles since the early 1970s and director of the UCLA-DOE Institute for Genomics & Proteomics since the early 1990s, as well as a member of the California NanoSystems Institute (CNSI) at UCLA.
Gregory A. Petsko is an American biochemist and member of the National Academy of Sciences, the National Academy of Medicine, the American Academy of Arts and Sciences, and the American Philosophical Society. He is currently Professor of Neurology at the Ann Romney Center for Neurologic Diseases at Harvard Medical School and Brigham and Women's Hospital. He formerly had an endowed professorship in Neurology and Neuroscience at Weill Cornell Medical College and is still an adjunct professor of Biomedical Engineering at Cornell University, and is also the Gyula and Katica Tauber Professor, Emeritus, in biochemistry and chemistry at Brandeis University.
Helen Miriam Berman is a Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University and a former director of the RCSB Protein Data Bank. A structural biologist, her work includes structural analysis of protein-nucleic acid complexes, and the role of water in molecular interactions. She is also the founder and director of the Nucleic Acid Database, and led the Protein Structure Initiative Structural Genomics Knowledgebase.
The Protein Structure Initiative (PSI) was a USA based project that aimed at accelerating discovery in structural genomics and contribute to understanding biological function. Funded by the U.S. National Institute of General Medical Sciences (NIGMS) between 2000 and 2015, its aim was to reduce the cost and time required to determine three-dimensional protein structures and to develop techniques for solving challenging problems in structural biology, including membrane proteins. Over a dozen research centers have been supported by the PSI for work in building and maintaining high-throughput structural genomics pipelines, developing computational protein structure prediction methods, organizing and disseminating information generated by the PSI, and applying high-throughput structure determination to study a broad range of important biological and biomedical problems.
Amit Prakash Sharma is an Indian parasitologist and Director of National Institute of Malaria Research, New Delhi. He is known for his studies on the disease of malaria and is an elected fellow of the Indian Academy of Sciences, Indian National Science Academy, The World Academy of Sciences and the National Academy of Sciences, India. He has been awarded the Shanti Swarup Bhatnagar Award in Biological Sciences, JC Bose Fellowship, Ranbaxy Science Research Award, Infosys Science Award in Biological Sciences, Om Prakash Bhasin Award in Biological Sciences and Lakshmipat Singhania- IIM Lucknow National Leadership Award.
Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. These models, which provide 3D coordinates for each atom in the molecule, come from structural biology experiments such as x-ray crystallography or nuclear magnetic resonance (NMR). The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties.
Mark S. Boguski was an American pathologist specializing in computational analysis and structural biology, He was elected in 2001 to the U.S. National Academy of Medicine, and was a Fellow of the American College of Medical Informatics.
Władysław Minor also known as Wladek Minor is a Polish-American biophysicist, a specialist in structural biology and protein crystallography. He is a Harrison Distinguished Professor of Molecular Physiology and Biological Physics at the University of Virginia. Minor is a co-author of HKL2000/HKL3000 – crystallographic data processing and structure solution software used to process data and solve structures of macromolecules, as well as small molecules. He is a co-founder of HKL Research, a company that distributes the software. He is also a co-author of a public repository of diffraction images (proteindiffraction.org) for some of the protein structures available in the Protein Data Bank and other software tools for structural biology.
Gaetano T. Montelione is an American biophysical chemist, Professor of Chemistry and Chemical Biology, and Constellation Endowed Chair in Structural Bioinformatics at Rensselaer Polytechnic Institute in Troy, NY.
References
- ↑ "Structural GenomiX Appoints Stephen K. Burley as Chief Scientific Officer -- re> SAN DIEGO, Oct. 16 /PRNewswire/ --". Archived from the original on 2014-10-13.
- ↑ "Introducing Professor Stephen K. Burley | Department of Chemistry & Chemical Biology". Archived from the original on 2014-10-14. Retrieved 2014-10-08.
- ↑ "Stocks".
- ↑ http://proteomics.rutgers.edu/public/?q=faculty/burley
- ↑ "Rutgers recruits top researcher to head Center for Integrative Proteomics Research - NJBIZ". 17 December 2012.
- ↑ "RCSB PDB - News". www.rcsb.org. Archived from the original on 2014-09-03.
- ↑ "Editorial Board | Oncogene".