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Database of recurrent RNA 3D structure motifs and their interactions (hydrogen bonds and close contacts), found in experimentally determined RNA structures and in RNA-protein complexes.
Currently you can find here over 2600 RNA structures and RNA-protein complexes from the PDB (see statistics for details). We hope that your favorite ones are in. If not, keep visiting us - the database is updated weekly.
CANCER is the leading cause of human mortality resulted in 7.9 million deaths in 2007 and projected to be over 11 million deaths in 2030 worldwide. LUNG CANCER is the most common cause of cancer-related mortality over the last 30 years accounted for 1.4 million deaths in 2008. Despite recent advances in diagnosis and treatment, the prognosis of lung cancer patients remains dismal with an overall 5-year survival of <15%. Discovery of novel targets and therapeutic strategies is urgently needed.
IGDB.NSCLC database is aiming to facilitate and prioritize identified lung cancer genes and microRNAs for pathological and mechanistic studies of lung tumorigenesis and for developing new strategies for clinical interventions. We integrated and curated various lung cancer genomic datasets to present
1. lung cancer genes with somatic mutations, experimental supports and statistic significance in association with clinicopathological features; 2. genomic alterations with copy number alterations (CNA) detected by high density SNP arrays, gain or loss regions detected by arrayed comparative genome hybridization (aCGH), and loss of heterozygosity (LOH) detected by microsatellite markers; 3. aberrant expression of genes and microRNAs detected by various microarrays.
IGDB.NSCLC database provides user friendly interfaces and searching functions to display multiple layers of evidence for detecting lung cancer target genes and microRNAs, especially emphasizing on concordant alterations:
1. genes with altered expression located in the CNA regions; 2. microRNAs with altered expression located in the CNA regions; 3. somatic mutation genes located in the CNA regions; and 4. genes associated with clinicopathological features located in the CNA regions.
PBmice is based on the April 2007 Mus musculus (strain C57BL/6J) high coverage assembly (NCBIm37,GCA_000001635.18
PDZBase is a manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. PDZBase currently contains 339 experimentally determined protein protein interactions. For more information, visit the PDZBase help pages or contact us at pdzbase@med.cornell.edu.
With over 115,000 described species, the order Hymenoptera comprises approximately 10% of the species diversity on Earth. The largest described family in the order, Icheumonidae, contains more species than all species of birds and mammals combined! This group of 'membrane-winged' insects includes sawflies, bees, ants and wasps, which directly affect human health and agriculture through diverse roles such as pollinators, pests and parasitoids.
The Hymenoptera Genome Database (HGD) is an informatics resource supporting genomics of insect species of this order. HGD provides access to the genomes of bees Apis mellifera, Bombus terrestris and B. impatiens, the parasitoid wasp Nasonia vitripennis, and seven species of ants available through the Ant Genomes Portal. It will soon incorporate genome databases for two additional species of bees, Apis dorsata and A. florea, as well as two additional species of ants. Combining these species into a single resource allows biologists to leverage the genome information, and enhances the value of genomic data for each species by facilitating cross-species comparisons.
Haematopoiesis (blood formation) has long served as a model process for studying stem cells and represents the best characterised adult stem cell system with functional assays and purification strategies for a plethora of precursors ranging from the pluripotent haematopoietic stem cell (HSC) via multipotent and unipotent progenitors to at least 14 distinct mature cell types. Transcriptional control is a key factor controlling haematopoiesis.
HOWDY (Human Organized Whole genome Database) is a database system for retrieve human genome information in different data sources that are available to public. Sources of HOWDY are 14 public databases. The information you could find here is automatically extracted from the genetic databases and shown with all data having the identifiers in common and linking to one another. HOWDY facilitates obtaining information of human genes by using official symbols and aliases. HOWDY is daily updated.
HOWDY: an integrated database system for human genome research. Hirakawa M. Nucleic Acids Research, 30:152-157, 2002
Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models.
Het-PDB Navi. is a navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms.
PDB is a database for protein three-dimensional structures, but the data in PDB are often obtained with bound non-standard components such as DNA, RNA, ATP, GTP, PLP and so forth. As number of proteins in PDB increases, we realized that a wealth of information for small molecule-protein interactions is buried in PDB.
The interactions found in PDB can be treated as a general template for interaction between a protein and a small molecule, such as ATP, GTP and drugs.
We have, hereby, launched Het-PDB Navi. as a starter for classification and data retrieval system of protein-small molecule interactions from PDB.
The database is focused on small molecules and does not treat macromolecules such as DNA and RNA. The database was initially developed at Nagoya University in 1999, and transferred to Nagahama Institute of Bio-Science and Technology in 2003.
The database has been maintained by Prof. Mitiko Go's laboratory from the beginning.
HEXEvent is a free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser . This list can be restricted by the user to either only a specific region in the genome (by specifying the chromosome, the strand and the start and end position), to a whole chromosome or to a group of genes. Furthermore, exons can be filtered according to their splicing type (constitutive exons, cassette exons and exons with one or more alternative 3' and/or 5' splice sites).
In order to extract a customized set of exons, the user-specific definitions of exon types can be fixed. The user needs to specify in what fraction of ESTs an exon is allowed to be alternatively spliced in order to still be called constitutive. Furthermore, the user can restrict the set of requested cassette exons by a certain upper inclusion level, which, for instance, is useful when only looking for low-inclusion exons.
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The Biomolecule Stretching Database (BSDB) contains information related to mechanical stretching of biomolecules. Currently, the database is restricted to proteins and to stretching at constant velocity.When plotting the force of resistance to pulling, F, versus the pulling distance, d, one may encounter one or more isolated force peaks on the way to full stretching. the characteristic scale of F is characterized byFmax - the maximum force in an isolated force peak. If no force peak develops, Fmax is assigned a value of zero. Usually, this happens when some disulphide bonds prevent full stretching.
The Database lists results obtained theoretically within a structure-based coarsegrained model, initially, for 17 134 structures with no more than 250 amino acids as discussed in reference: M. Sikora, J. I. Sułkowska, and M. Cieplak, Mechanical strength of 17 134 model proteins and cysteine slipknots, PLoS Computational Biology, 5 e1000547 (2009). The database is further described in: M. Sikora, J. I. Sulkowska, B. S. Witkowski, and M. Cieplak, BSDB: the biomolecule stretching database, Nucl. Acid Res. 39, D443-D450 (2011).
Multi-domain proteins are discussed in reference: M. Sikora and M. Cieplak. Mechanical stability of multi-domain proteins and novel mechanical clamps, Proteins: Struct. Funct., and Bioinf. 79(6) 2011, where 315 proteins are considered.
In the first two papers, we have used terms "cysteine knot" and "cysteine slipknots" instead of the correct terms "cystine knot" and "cystine slipknot" respectively. Further analysis of the cystine slipknot proteins can be found in reference: L. Peplowski, M. Sikora, W. Nowak, and M. Cieplak, Molecular jamming - the cystine slipknot mechanical clamp in all-atom simulations, J. Chem. Phys. 134, 085102 (2011).
It also lists experimental results on Fmax that are available in the literature. Furthermore, it provides information on Fmax as obtained within all-atom simulations. The users are encouraged to submit new theoretical and experimental entries to us and to request calculations for proteins that are not yet stored in BSDB.
The mission of the Integrated Microbial Genomes (IMG) system is to support the annotation, analysis and distribution of microbial genome and metagenome datasets sequenced at DOE's Joint Genome Institute (JGI). IMG is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and metagenome datasets, as long as they agree with the IMG data release policy and follow the metadata requirements for integrating data into IMG (IMG submission site).
IGRhCellID database integrates 7 common authentic tools from public domains and profiles of genomic alterations from our laboratory of common human cell lines to reduce or eradicate long standing concerns of cell misidentification. Moreover, profiles of genomic alterations of common human cell lines further allow users to select cell lines with designated genetic background. For examples, users can select a cell line with homozygous deletion of a gene to serve as indigenous knock-out human cell model, with amplification of a gene to serve as cell model for therapeutic drug testing, and with common alterations in multiple human cell lines for common altered cancer genes across cancer types.
The purpose of this database is to represent the relationship between protein structural change and ligand binding. We classified protein structural changes into 7 classes blow, in terms of the ligand binding sites and the location where the dominant motion occurs.
A database of protein-protein interactions mediated by interchain ß-sheet formation
This browser enables access to the diploid genome sequence of J. Craig Venter as recently published in PLoS Biology. The graphical interface depicts the haploid sequence with SNP and insertion/deletion DNA variants as identified by genome assembly and comparison methods. The interface also represents the haplotype blocks from which diploid genome sequence can be inferred and gene annotations. This work was done at the J. Craig Venter Institute, with collaborators from The Hospital for Sick Children in Toronto, Canada, University of California, San Diego, and Universidad de Barcelona, Spain.
A database of signatures of natural selection in the human genome
The two-chain protein interface in our definition was composed of interacting residues and nearby residues, respectively. The interfaced residues was picked up first. If the distance of any two atoms between residues is less than their sum of van der Waals radii plus 0.5 Angstrom, both residues were registered as the interfaced residues. When assigned interface residues was less than 10 residues, an arbitrary but reasonable number to reflect the minimum requirement of contact, the interface was considered as a result of crystal packing force. Therefore, it would not be considered further. To enable illuminating the types of architectures at the interface, residues whose alpha carbon atom is within a distance of 6.0 Angstrom from an alpha carbon atom of previous assigned interface residues, are included and named nearby residue. The 6.0 Angstrom selected from trial and error is very close to the lowest distance to include residues not involving in interface but essential for demonstrating the scaffold of the interface.
In this study, we have surveyed exhaustively the structures of protein-protein interfaces in PDB to carry out the structural comparisons of the interfaces. This works is an extension of the Nussinov and coworkers study (Tsai et al, 1996)
HIVdb: a database of the structures of human immunodeficiency virus protease.
HitPredict is a resource of high confidence protein-protein interactions. Interactions can be searched and downloaded with their predicted confidence level.
Protein-protein interactions from IntAct, BIOGRID and HPRD are combined, annotated and assigned a reliability score in order to identify a high confidence subset.
The reliability score is calculated as the Likelihood Ratio using naive Bayesian networks combining sequence, structure and functional annotations of the interacting proteins.
HitPredict has 239584 protein-protein interactions across 9 species, 168458 of which are predicted to be of high confidence.
Retroviral genomes or parts of their genomes are present in the DNA of many organisms. Studies of endogenous retroviral nucleotide sequences have become an important part of contemporary retrovirology as well as of molecular and cellular biology and genomics. Human endogenous retroviruses (HERVs) are of special interest also because their expression may be associated with several diseases, including cancer. Various groups of HERVs have been reported in the human genome. Their number can range from one copy to many thousand copies.
This database is compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects. We created a relatively simple and fast environment for screening human genome for HERVs. This makes it possible to continuously improve classification and characterization of retroviral families. The HERV database now contains retroviruses from more than 90 % of the human genome.
Start your search by clicking on the Search link below. You can search by HERV families, chromosome positions and several other features. For explanation of abbreviations click on Help. The Fasta search or Blat search are used for comparing your nucleotide sequence against all HERVs in the database. For abbreviations click onHelp. An example of using the database is given below, click Example to check.
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