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*  SWISS-MODEL | Documentation
The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide. ... SWISS-MODEL is a fully automated protein structure homology-modelling server. ... The SWISS-MODEL template library is a large structural database of experimentally determined protein structures derived from ... structures and structures determined with electron microscopy, as the latter determines the overall shape of the molecule not ...
  https://swissmodel.expasy.org/docs/help
*  Chimera-Related Databases and Software
Databases ASTRAL. Experimentally determined protein structures, divided into domains as defined by SCOP (Structural ... RCSB Protein Data Bank (PDB), Protein Data Bank in Europe (PDBe), Protein Data Bank Japan (PDBj) Experimentally determined ... A database of human nonsynonymous single-nucleotide polymorphisms (nsSNPs) mapped onto protein structures. Chimera-generated ... Assignment of NMR spectra for determining protein and nucleic acid structures. Uses Chimera to display NMR peak assignments on ...
  http://www.cgl.ucsf.edu/chimera/related/related.html
*  Protein structure database - Wikipedia
... a protein structure database is a database that is modeled around the various experimentally determined protein structures. The ... is a database of similar protein-protein interfaces in crystal structures of homologous proteins. Protein the NIH protein ... The Protein Data Bank (PDB) was established in 1971 as the central archive of all experimentally determined protein structure ... the data has been used in various other protein structure databases. Examples of protein structure databases include (in ...
  https://en.wikipedia.org/wiki/Protein_structure_database
*  TR-09-03 Calculating All Pairwise Similarities from the RCSB Protein Data Bank: Client/Server Work Distribution on the Open...
Proteins can have various degrees of similarity. If two proteins show high similarity in their ... Calculating All Pairwise Similarities from the RCSB Protein Data Bank: Client/Server Work Distribution on the Open Science Grid ... is a leading primary database that provides access to experimentally determined protein structures, nucleic acids, and complex ... While protein sequence comparisons can be computed quickly, the calculation of protein structure alignments is much more time ...
  http://renci.org/technical-reports/tr-09-03/
*  FTBO Anti Vibration Plate with Integrated Power Model,ESC,PDB,5V 12V BEC pdb board for APM2.5/2.6/2.8&PIXHAWK Flight...
Protein Data Bank Japan maintains the database for experimentally determined protein structures: the PDB. PDBj annotates ... 01/ RCSB Protein Data Bank - RCSB PDB. The PDB archive contains information about experimentally-determined structures of ... The Protein Data Bank (PDB) is an archive of experimentally determined three-. dimensional structures of biological ... Align two protein structures in 3D space to produce a combined structure with the two overlayed. Structures can be obtained by ...
  http://actressimages.info/pactres13939.html
*  A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes | SpringerLink
In addition to the catalog of family members, the database provides experimentally determined 3D protein structures, ... is a structured database dedicated to the CAZy database family GH16 glycoside hydrolases [28]. The database is composed of 260 ... general databases, species-specific databases and family-specific databases. For each database, we describe the covered species ... Family-Specific Databases. Similar to species-specific databases, family-specific databases focus on a specific cell wall- ...
  https://link.springer.com/article/10.1007%2Fs12155-010-9082-6
*  Search NCBI databases - NCBI
Search all biomedical databases provided by the National Center for Biotechnology Information (NCBI), an agency of the U.S. ... Functional categorization of proteins by domain architecture. Structure. Experimentally-determined biomolecular structures ... Proteins. Protein sequences, 3-D structures, and tools for the study of functional protein domains and active sites ... Protein Clusters. Sequence similarity-based protein clusters. Sparcle. ...
  https://www.ncbi.nlm.nih.gov/search/?dr=citation&holding=chcnlib,chcnlib_fft,ohiolinklib,ucmclib
*  National Center for Biotechnology Information - Wikipedia
The Structure database of NCBI contains 3D coordinate sets for experimentally-determined structures in PDB that are imported by ... There is another database in protein known as Protein Clusters database which contains sets of proteins sequences that are ... Protein[edit]. Protein database maintains the text record for individual protein sequences, derived from many different ... Other databases: Protein Data Bank, Ensembl and InterPro. *Specialised genomic databases: BOLD, Saccharomyces Genome Database, ...
  https://en.wikipedia.org/wiki/National_Center_for_Biotechnology_Information
*  Molecular biology
... "experimentally determined three-dimensional biomolecular structures" of macromolecules obtained from the Brookhaven Protein ... "macromolecular structures." Included among the images are RNA structures from the protein database at the Brookhaven National ... Databases (6) Dictionaries (2) Periodicals (7) Problems, exercises, etc. (1) Research (3) Scholarships, fellowships, etc. (1) ... as well as over 250 DNA and protein structures. Sequence and... ... The Molecular Modelling Database (MMDB) NCBI, the National ...
  https://scout.wisc.edu/archives/b3052/molecular_biology
*  A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database | Genome Biology...
The database also contains the largest available collection of atomic models of phosphorylatable proteins. Detailed analysis of ... These models have been automatically built by homology to experimentally determined structures using a conservative procedure ... The database also contains structural information on those modified protein domains for which the actual structure, or the ... The sequence set of determined structures was obtained from Protein Data Bank (PDB) co-ordinates [76]. Positions for which no ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-5-r90
*  Molecular Modeling Database - Wikipedia
The Molecular Modeling Database (MMDB) is a database of experimentally determined three-dimensional biomolecular structures and ... Protein structure Madej, Thomas; Addess Kenneth J; Fong Jessica H; Geer Lewis Y; Geer Renata C; Lanczycki Christopher J; Liu ... 3D structures and macromolecular interactions". Nucleic Acids Res. England. 40 (Database issue): D461-4. doi:10.1093/nar/ ... https://www.ncbi.nlm.nih.gov/structure. ...
  https://en.wikipedia.org/wiki/Molecular_Modeling_Database
*  "Protein-protein interface: database, analysis and prediction" by Feihong Wu
486 protein-protein interfaces from experimentally determined protein complex structures in the current version of Protein Data ... Identification of protein-protein interaction sites is important to identification of protein functions, improvement of protein ... The research work focuses on three parts: We have built a Protein-Protein Interface Database (PPIDB) which extracted 71, ... Attempts are made to apply the NB PPIPS in a two stage prediction of protein-protein interfaces when only protein sequence is ...
  https://lib.dr.iastate.edu/etd/10955/
*  Discipline-Based Data Archives · University of Minnesota Libraries
Protein DataBank - Experimentally determined structures for macromolecules (protein and nucleic acids). The site includes ... It contains smaller databases for specific plants (e.g., BarleyBase) as well as a variety of related tools. ... The Cell: An Image Library - Images of all cell types from all organisms, including intracellular structures and movies or ... Extragalactic Database - NASA's archive of data for over 3 million extragalactic objects ...
  https://www.lib.umn.edu/datamanagement/datacenters
*  Bujnicki lab - Statistical potentials
... use a coarse-grained representation for both RNA and protein molecules and are capable of dealing with RNA structures with ... DARS-RNP showed the highest ability to identify native-like structures. ... knowledge-based potentials for scoring protein-RNA models obtained by docking: the quasi-chemical potential (QUASI-RNP) and the ... is an online database of representative experimentally determined and computationally predicted structures of proteins of the ...
  http://genesilico.pl/software/stand-alone/statistical-potentials
*  Bujnicki lab - PROTMAP2D
... is an online database of representative experimentally determined and computationally predicted structures of proteins of the ... RNA Bricks is a database of RNA 3D structure motifs and their contacts, both with themselves and with proteins. The database ... protein structures. It is a gateway to a number of methods for evaluation of protein structure (ANOLEA, PROSAII, PROVE or ... DATABASES * REPAIRtoire * REPAIRtoire is an online database for systems biology of DNA damage and repair. The database collects ...
  http://genesilico.pl/software/stand-alone/protmap2d
*  Bujnicki lab - SERVERS
... is an online database of representative experimentally determined and computationally predicted structures of proteins of the ... RNA Bricks is a database of RNA 3D structure motifs and their contacts, both with themselves and with proteins. The database ... protein structures. It is a gateway to a number of methods for evaluation of protein structure (ANOLEA, PROSAII, PROVE or ... protein structures. It is a gateway to a number of methods for evaluation of protein structure (ANOLEA, PROSAII, PROVE or ...
  http://genesilico.pl/software/servers
*  National Center for Biotechnology Information - Mashpedia Free Video Encyclopedia
The Structure database of NCBI contains 3D coordinate sets for experimentally-determined structures in PDB that are imported by ... Protein[edit]. Protein database is an important protein resource at NCBI. It maintains the text record for individual protein ... There is another database in protein known as Protein Clusters database which contains sets of proteins sequences that are ... Other databases: Protein Data Bank, Ensembl and InterPro. *Specialised genomic databases: BOLD, Saccharomyces Genome Database, ...
  http://www.mashpedia.com/National_Center_for_Biotechnology_Information
*  What is Molecular Graphics? (with pictures)
... in which experimentally-determined information about the structures of nucleic acids, proteins, and complex assemblies are ... As of 27 April 2010, there were 64,932 structures in the database. The RCSB popularizes their function with an invitation to ... The RCSB also sponsors protein modeling trials at regional Science Olympiads in the United States. The Worldwide Protein Data ... One key use of molecular graphics is in the study of proteins and nucleic acids. The Research Collaboratory for Structural ...
  http://www.wisegeek.com/what-is-molecular-graphics.htm
*  Biomolecular Recognition with Artificial Alpha Helices - Paramjit Arora
... proteins, RNA, DNA, and carbohydrates). Alpha-helices, ubiquitous elements of pr... ... 2) We will construct a database of experimentally determined structures of helix-mediated protein-protein interactions and ... Watkins, Andrew M; Arora, Paramjit S (2015) Structure-based inhibition of protein-protein interactions. Eur J Med Chem 94:480-8 ... Watkins, Andrew M; Wuo, Michael G; Arora, Paramjit S (2015) Protein-Protein Interactions Mediated by Helical Tertiary Structure ...
  http://grantome.com/grant/NIH/R01-GM073943-08
*  Sorting nexin-21 is a scaffold for the endosomal recruitment of huntingtin | Journal of Cell Science
Both lines represent known interactions from curated databases (pink) and those that have been experimentally determined ( ... Larger nodes represent proteins of known or predicted 3D structure. (C) Representative western analysis of HEK293-T cells ... defined by those proteins 100-fold enriched and with a protein score of ,50) identified a network of experimentally defined ... 2008). Protein networks supporting AP-3 function in targeting lysosomal membrane proteins. Mol. Biol. Cell. 19, 1942-1951. doi: ...
  http://jcs.biologists.org/content/131/17/jcs211672
*  Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean...
The LRR domain of the GmRLK18-1 protein formed both a monomer and a homo-dimer. The LRR domain bound avidly to 4 different CLE ... The aims here were to evaluate the LRRs ability to; homo-dimerize; bind larger proteins; and bind to small peptides. Western ... The protein encoded by GmRLK18-1 (Glyma_18_02680 on chromosome 18) was a receptor like kinase (RLK) encoded within the soybean ... analysis suggested homo-dimers could form after protein extraction from roots. The purified LRR domain, from residue 131-485, ...
  https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-13-43
*  Prediction of chemical-protein interactions: multitarget-QSAR versus computational chemogenomic methods - Molecular BioSystems ...
It is time-consuming and costly to determine CPI experimentally, and computational methods will facilitate the determination of ... In this study, two methods, multitarget quantitative structure-acti ... Elucidation of chemical-protein interactions (CPI) is the basis of target identification and drug discovery. ... Two comprehensive data sets were collected from the ChEMBL database for method assessment. One data set consisted of 81 689 CPI ...
  http://pubs.rsc.org/en/content/articlelanding/2012/mb/c2mb25110h
*  World Community Grid - Research - OpenZika
Screen millions of compounds against experimentally determined Zika protein structures, as soon as these are known. ... Screen compounds from the ZINC database, a collection of millions of compounds for virtual screening, against Zika protein ... As additional and more accurate Zika-related protein structures are determined, such structures will also be used as targets ... This often begins with determining the "crystal structure," at the atomic scale, of these key proteins, then screening chemical ...
  https://www.worldcommunitygrid.org/research/zika/details.do
*  Integrated Resource for Protein Recognition Studies - Ilya Vakser
The 3D structure of a protein-protein complex, g... ... The protein-protein docking problem is one of the focal points ... The database of experimentally determined and simulated unbound complexes will be further expanded upon the core dataset. It ... The 3D structure of a protein-protein complex, generally, is more difficult to determine experimentally than the structure of ... The development will make use of the rapidly growing body of experimentally determined structures of protein-protein complexes ...
  http://grantome.com/grant/NIH/R01-GM074255-09A1
*  UniProtKB/Swiss-Prot Release 2018 10 statistics
The average sequence length in UniProtKB/Swiss-Prot is 359 amino acids. The shortest sequence is GWA_SEPOF (P83570): 2 amino acids. The longest sequence is TITIN_MOUSE (A2ASS6): 35213 amino acids. 4. JOURNAL CITATIONS Note: the following citation statistics reflect the number of distinct journal citations. Total number of journals cited in this release of UniProtKB/Swiss-Prot: 2753 4.1 Table of the frequency of journal citations Journals cited 1x: 866 2x: 391 3x: 163 4x: 136 5x: 110 6x: 100 7x: 66 8x: 56 9x: 37 10x: 33 11- 20x: 219 21- 50x: 227 51-100x: 118 ,100x: 231 4.2 List of the most cited journals in UniProtKB/Swiss-Prot Nb Citations Journal name -- --------- ------------------------------------------------------------- 1 24439 Journal of Biological Chemistry 2 11326 Proceedings of the National Academy of Sciences of the U.S.A. 3 6606 Journal of Bacteriology 4 5619 Biochemical and Biophysical Research Communications 5 5312 Biochemistry 6 4984 Nucleic Acids Research 7 4816 FEBS Letters 8 ...
  https://web.expasy.org/docs/relnotes/relstat.html
*  RCSB Protein Data Bank - RCSB PDB
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
  https://www.rcsb.org/pdb/home/home.do
*  RCSB Protein Data Bank - RCSB PDB
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
  http://www.rcsb.org/pdb/home/home.do
*  Protein Data Bank - Wikipedia
PDB setzte sich ursprünglich aus Proteinstrukturen aus der Röntgen-Kristallstrukturanalyse und dem 1968 gegründeten Brookhaven RAster Display (BRAD) zusammen. Im Jahr 1969, entstand unter der Förderung durch Walter Hamilton am Brookhaven National Laboratory und der Urheberschaft von Edgar Meyer (Texas A&M University) eine Software zur Speicherung von Atomkoordinaten in einem gemeinsamen Format. Im Jahr 1971 wurde die Suchfunktion SEARCH eingeführt, mit der die Daten heruntergeladen und offline gespeichert werden konnten.[3] Nach Hamiltons Tod 1973 übernahm Tom Koeztle die Leitung für die folgenden 20 Jahre. Im Jahr 1994 ging die Führung an Joel Sussman über. Von Oktober 1998 bis Juni 1999 wurde PDB in das Research Collaboratory for Structural Bioinformatics (RCSB) übertragen.[4][5] Dort wurde Helen M. Berman of Rutgers University neue Direktorin.[6] Im Jahr 2003 wurde PDB mit der Gründung von Worldwide Protein Data Bank (wwPDB) ...
  https://de.wikipedia.org/wiki/Protein_Data_Bank
*  Search | re3data.org
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The ...
  https://www.re3data.org/search?contentTypes%5B%5D=Scientific%20and%20statistical%20data%20formats
*  UniProtKB/Swiss-Prot 2012 10
2. TAXONOMIC ORIGIN Total number of species represented in this release of UniProtKB/Swiss-Prot: 12922 The first twenty species represent 112553 sequences: 20.9 % of the total number of entries. 2.1 Table of the frequency of occurrence of species Species represented 1x: 5426 2x: 1882 3x: 981 4x: 639 5x: 466 6x: 381 7x: 284 8x: 217 9x: 199 10x: 123 11- 20x: 668 21- 50x: 403 51-100x: 212 ,100x: 1041 2.2 Table of the most represented species ------ --------- -------------------------------------------- Number Frequency Species ------ --------- -------------------------------------------- 1 20233 Homo sapiens (Human) 2 16566 Mus musculus (Mouse) 3 11571 Arabidopsis thaliana (Mouse-ear cress) 4 7815 Rattus norvegicus (Rat) 5 6621 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 6 5965 Bos taurus (Bovine) 7 5089 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) 8 4431 Escherichia coli (strain K12) 9 4188 Bacillus subtilis (strain 168) 10 4126 Dictyostelium ...
  http://www.uniprot.org/statistics/Swiss-Prot%202012_10
*  UniProtKB/Swiss-Prot 2012 02
2. TAXONOMIC ORIGIN Total number of species represented in this release of UniProtKB/Swiss-Prot: 12726 The first twenty species represent 111314 sequences: 20.8 % of the total number of entries. 2.1 Table of the frequency of occurrence of species Species represented 1x: 5365 2x: 1849 3x: 955 4x: 628 5x: 463 6x: 374 7x: 272 8x: 218 9x: 198 10x: 110 11- 20x: 655 21- 50x: 392 51-100x: 209 ,100x: 1038 2.2 Table of the most represented species ------ --------- -------------------------------------------- Number Frequency Species ------ --------- -------------------------------------------- 1 20246 Homo sapiens (Human) 2 16473 Mus musculus (Mouse) 3 11018 Arabidopsis thaliana (Mouse-ear cress) 4 7690 Rattus norvegicus (Rat) 5 6619 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 6 5885 Bos taurus (Bovine) 7 4976 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) 8 4431 Escherichia coli (strain K12) 9 4244 Bacillus subtilis 10 4122 Dictyostelium discoideum (Slime ...
  http://www.uniprot.org/statistics/Swiss-Prot%202012_02
*  Data Deposition | JCB
For molecular models, the peptide backbone coordinates plus the coordinates of important side chains emphasized in the text should be made available in a worldwide Protein Data Bank (PDB) member. We encourage authors to deposit structural data of biological macromolecules obtained by 3D electron mcroscopy in the EMDataBank or the Protein Data Bank in Europe.. Protein sequence and functional information can be deposited in Uniprot.. Nucleic acid structural information should be submitted to the Nucleic Acid Database (NDB). For NMR structures, data deposited should include resonance assignments, all restraints used in structure determination (NOEs, spin-spin coupling constants, amide exchange rates, etc.), and the derived atomic coordinates for both an individual structure and for a family of acceptable structures.. Mass spectrometry data should be deposited in a ...
  http://d2j7maqgsavdlx.cloudfront.net/data-deposition
*  Summary of the gene family classification of four relat | Open-i
Summary of the gene family classification of four related species, Cyclina sinensis, Crassostrea gigas, Lottia gigantea and Capitella teleta.Only putative pepti
  https://openi.nlm.nih.gov/detailedresult.php?img=PMC4390376_pone.0123296.g003&req=4
*  Patent US20040059731 - Multistage intelligent database search method - Google Patents
An improved multistage intelligent database search method includes (1) a prefilter that uses a precomputed index to compute a list of most
  http://www.google.com/patents/US20040059731?dq=6,654,957
*  PROTEINS OF KNOWN STRUCTURE BY SOLID-STATE NMR
The table below provides information about proteins whose structures have been determined by solid-state NMR, to a resolution sufficient to have resulted in a file deposited with the worldwide Protein Data Bank (wwPDB). Here is the NMR page of the wwPDB ...
  http://www.drorlist.com/nmr/SPNMR.html
*  Genes | Free Full-Text | Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction...
In view of the fact that appearance of novel protein domain architectures (DA) is closely associated with biological innovations, there is a growing interest in the genome-scale reconstruction of the evolutionary history of the domain architectures of multidomain proteins. In such analyses, however, it is usually ignored that a significant proportion of Metazoan sequences analyzed is mispredicted and that this may seriously affect the validity of the conclusions. To estimate the contribution of errors in gene prediction to differences in DA of predicted proteins, we have used the high quality manually curated UniProtKB/Swiss-Prot database as a reference. For genome-scale analysis of domain architectures of predicted proteins we focused on RefSeq, EnsEMBL and NCBI's GNOMON predicted sequences of Metazoan species with completely sequenced genomes. Comparison of the DA of ...
  http://www.mdpi.com/2073-4425/2/3/449/htm
*  Protein Identifier Cross-Reference Service
The Protein Identifier Mapping Service provides a free interface to resolve protein identifiers across multiple databases that correspond to the same logical protein.
  https://www.ebi.ac.uk/Tools/picr/WSDLDocumentation.do
*  What enzyme catalyzes the elongation of a new DNA strand? | Reference.com
The enzyme that catalyzes the elongation of a DNA strand is DNA polymerase, according to the RCSB Protein Data Bank. This enzyme adds to the growing DNA molecule by adding nucleotide bases. DNA...
  https://www.reference.com/science/enzyme-catalyzes-elongation-new-dna-strand-322f2684fbe800b9
*  Animal Abuse Database - Search Results | Pet-Abuse.Com Animal Cruelty Database
There are 330 cases currently listed in Australia. Results are displayed 25 per page. Login or create an account for additional advocacy tools, including e-mail notifications when updates are posted to selected cases.. Pages: 1 2 3 4 5 6 7 8 9 10 Next» ...
  http://www.pet-abuse.com/pages/cruelty_database/results.php?country=AU&au_state=ALL&sort=crime&order=asc&page=1
*  Animal Abuse Database - Search Results | Pet-Abuse.Com Animal Cruelty Database
There are 509 cases currently listed in the US state of VA. Results are displayed 25 per page. Login or create an account for additional advocacy tools, including e-mail notifications when updates are posted to selected cases.. Pages: «Prev 6 7 8 9 10 11 12 13 14 15 Next» ...
  http://www.pet-abuse.com/pages/cruelty_database/results.php?country=US&us_state=VA&order=desc&page=10
*  Protein Data Bank Japan - PDB Japan - PDBj
Protein Data Bank Japan maintains the database for experimentally determined protein structures: the PDB. PDBj annotates deposited structures, provides additional annotations and offers various services to search for and analyze deposited structures.
  http://www.pdbj.org
*  APD2: the updated antimicrobial peptide database and its application in peptide design.
Abstract The antimicrobial peptide database (APD, http://aps.unmc.edu/AP/main.php) has been updated and expanded. It now hosts 1228 entries with 65 anticancer, 76 antiviral (53 ant..
  https://www.omicsonline.org/references/apd2-the-updated-antimicrobial-peptide-database-and-its-application-in-peptide-design-810729.html
*  Course: Inside protein databases: bridging sequences and knowledge - March 2017
08h30 Protein sequence databases: theory. 10h30 COFFEE BREAK. 11h00 Controlled vocabularies and standardization resources: theory. 12h15 LUNCH. 13h30 Protein sequence databases and Gene Ontology: practicals. 15h00 COFFEE BREAK. 15h30 Analysis tools using ontologies : theory. 16h00 Protein sequence databases and Gene Ontology: practicals. 17h00 Evaluation / Exam. 18h00 END ...
  https://edu.sib.swiss/course/view.php?id=44
*  quotations | Bioinformatics and Genomics Department at CIPF
Newswise - La Jolla, Calif., October 20, 2015 - In a collaborative study led by Sanford Burnham Prebys Medical Discovery Institute (SBP), researchers have combined two publicly available 'omics' databases to create a new catalogue of 'cancer drivers'. Cancer drivers are genes that when altered, are responsible for cancer progression. The researchers used cancer mutation and protein structure databases to identify mutations in patient tumors that alter normal protein-protein interaction (PPI) interfaces. ...
  http://bioinfo.cipf.es/taxonomy/term/140
*  Current Protein & Peptide Science, Volume 8 - Number 4
Current Protein & Peptide Science covers a field by discussing research from the leading laboratories in a field and should pose questions for futu...
  https://benthamscience.com/journals/current-protein-and-peptide-science/volume/8/issue/4/
*  Current Protein & Peptide Science, Volume 9 - Number 2
Current Protein & Peptide Science covers a field by discussing research from the leading laboratories in a field and should pose questions for futu...
  https://benthamscience.com/journals/current-protein-and-peptide-science/volume/9/issue/2/
*  Index of /wrpearson/fasta/PUBS/gonzalez09a/refprotdom1.1
75% of the Pfam model length. long_domain=1 sequences are found in library_long_domains.fa.gz and in library_all_domains.fa.gz non_redundant Useful to calculate family size "0" flags a redundant domain that overlaps with another with longer sequence homology annotation "1" flags the non-redundant domain with the longer sequence homology annotation ======================= 3. Supplementary Annotation files ================================== pfam_to_clan.txt - Lists the pfam family to clan superfamily correspondence. Note: The annotations on this database are at the superfamily level, which we recommend for homology evaluation. See the FAQ.txt and (Gonzalez and Pearson, NAR, 2010) for more details of why coalescing superfamilies is the preferred choice when evaluating homology. refprotdom_domain_bound_ext.txt - Lists the domains that in pfam v.21 were annotated as partial homologies whose coordinates we extended. Current uniprot accessions and sequence ids are provided, as well as the corresponding ...
  http://faculty.virginia.edu/wrpearson/fasta/PUBS/gonzalez09a/refprotdom1.1/
*  Bioinformatics Papers
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. The complete paper is available on-line by following links from the PubMed website ...
  http://globin.cse.psu.edu/courses/fall2000/papers.html
*  PDB 1zlm function and biology ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
1zlm: Function and biology annotation of Crystal structure of the SH3 domain of human osteoclast stimulating factor. Includes SCOP, CATH, InterPro, GO and Intenz annotation.
  http://www.ebi.ac.uk/pdbe/entry/pdb/1zlm/biology