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Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 36.0, was released in September 2023 and contains 20,795 families.
Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry. The individual resources are hosted in a decentralized way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions.
Implicit solvation is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes.
Protein subfamily is a level of protein classification, based on their close evolutionary relationship. It is below the larger levels of protein superfamily and protein family.
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Biology Monte Carlo methods (BioMOCA) have been developed at the University of Illinois at Urbana-Champaign to simulate ion transport in an electrolyte environment through ion channels or nano-pores embedded in membranes. It is a 3-D particle-based Monte Carlo simulator for analyzing and studying the ion transport problem in ion channel systems or similar nanopores in wet/biological environments. The system simulated consists of a protein forming an ion channel (or an artificial nanopores like a Carbon Nano Tube, CNT), with a membrane (i.e. lipid bilayer) that separates two ion baths on either side. BioMOCA is based on two methodologies, namely the Boltzmann transport Monte Carlo (BTMC) and particle-particle-particle-mesh (P3M). The first one uses Monte Carlo method to solve the Boltzmann equation, while the later splits the electrostatic forces into short-range and long-range components.
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Donna R. Maglott is a staff scientist at the National Center for Biotechnology Information known for her research on large-scale genomics projects, including the mouse genome and development of databases required for genomics research.
Teresa Lyn Head-Gordon is an American chemist and the Chancellor's Professor of Chemistry, Bioengineering, and Chemical and Biomolecular Engineering at the University of California, Berkeley. She is also a faculty scientist in the Chemical Sciences Division at the Lawrence Berkeley National Laboratory and a fellow of both the American Institute for Medical and Biological Engineering and the American Chemical Society (ACS).
David S. Wishart is a Canadian researcher and a Distinguished University Professor in the Department of Biological Sciences and the Department of Computing Science at the University of Alberta. Wishart also holds cross appointments in the Faculty of Pharmacy and Pharmaceutical Sciences and the Department of Laboratory Medicine and Pathology in the Faculty of Medicine and Dentistry. Additionally, Wishart holds a joint appointment in metabolomics at the Pacific Northwest National Laboratory in Richland, Washington. Wishart is well known for his pioneering contributions to the fields of protein NMR spectroscopy, bioinformatics, cheminformatics and metabolomics. In 2011, Wishart founded the Metabolomics Innovation Centre (TMIC), which is Canada's national metabolomics laboratory.
IntFOLD is fully automated, integrated pipeline for prediction of 3D structure and function from amino acid sequences. The pipeline is wrapped up and deployed as a Web Server. The core of the server method is quality assessment using built-in accuracy self-estimates (ASE) which improves performance prediction of 3D model using ModFOLD.
References
- ↑ Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E.; Brookes, David H.; Wilson, Leighton; Chen, Jiahui (2017-08-24). "Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite". Protein Science. 27 (1): 112–128. doi:10.1002/pro.3280. PMC 5734301 . PMID 28836357.
- ↑ McCammon, J. Andrew; Holst, Michael J.; Joseph, Simpson; Sept, David; Baker, Nathan A. (2001-08-28). "Electrostatics of nanosystems: Application to microtubules and the ribosome". Proceedings of the National Academy of Sciences. 98 (18): 10037–10041. Bibcode:2001PNAS...9810037B. doi: 10.1073/pnas.181342398 . ISSN 0027-8424. PMC 56910 . PMID 11517324.
- ↑ Baker, Nathan A.; McCammon, J. Andrew; Nielsen, Jens E.; Dolinsky, Todd J. (2004-07-01). "PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations". Nucleic Acids Research. 32 (suppl_2): W665–W667. doi:10.1093/nar/gkh381. ISSN 0305-1048. PMC 441519 . PMID 15215472.
- ↑ Baker, Nathan A.; Klebe, Gerhard; Jensen, Jan H.; Nielsen, Jens E.; Li, Hui; Czodrowski, Paul; Dolinsky, Todd J. (2007-07-01). "PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations". Nucleic Acids Research. 35 (suppl_2): W522–W525. doi:10.1093/nar/gkm276. ISSN 0305-1048. PMC 1933214 . PMID 17488841.
- ↑ "PQR molecular structure format — APBS-PDB2PQR 1.6 documentation". apbs-pdb2pqr.readthedocs.io. Retrieved 2019-05-23.
