The binding database: overview and user's guide

The large and growing body of experimental data on molecular binding is of enormous value in biology, pharmacology, and chemistry. Applications include the assignment of function to biomolecules, drug discovery, molecular modeling, and nanotechnology. However, binding data are difficult to find and access because they are available almost exclusively through scientific journals. BindingDB, a public, web-accessible database of measured binding affinities, is designed to address this problem. BindingDB collects data for natural and modified biomolecules and for synthetic compounds, and provides detailed experimental information. Currently, measurements by isothermal titration calorimetry are fully supported; measurements by enzyme inhibition will soon be included as well. The web site allows data to be searched by a range of criteria, including binding thermodynamics, sequence homology, and chemical structure, substructure, and similarity. Experimentalists are encouraged to publicize their data by entering it into BindingDB via the online forms. Such data can be updated or revised by the depositor, if necessary, and will remain publicly accessible. User involvement and feedback are welcomed.     

CVD: the intestinal crypt/villus in situ hybridization database

The intestinal crypt/villus in situ hybridization database (CVD) query interface is a web-based tool to search for genes with similar relative expression patterns along the crypt/villus axis of the mammalian intestine. The CVD is an online database holding information for relative gene expression patterns in the mammalian intestine and is based on the scoring of in situ hybridization experiments reported in the literature. CVD contains expression data for 88 different genes collected from 156 different in situ hybridization profiles. The web-based query interface allows execution of both single gene queries and pattern searches. The query results provide links to the most relevant public gene databases. AVAILABILITY: http://pc113.imbg.ku.dk/ps/     

Strategies for the effective identification of remotely related sequences in multiple PSSM search approach

Searches using position specific scoring matrices (PSSMs) have been commonly used in remote homology detection procedures such as PSI-BLAST and RPS-BLAST. A PSSM is generated typically using one of the sequences of a family as the reference sequence. In the case of PSI-BLAST searches the reference sequence is same as the query. Recently we have shown that searches against the database of multiple family-profiles, with each one of the members of the family used as a reference sequence, are more effective than searches against the classical database of single family-profiles. Despite relatively a better overall performance when compared with common sequence-profile matching procedures, searches against the multiple family-profiles database result in a few false positives and false negatives. Here we show that profile length and divergence of sequences used in the construction of a PSSM have major influence on the performance of multiple profile based search approach. We also identify that a simple parameter defined by the number of PSSMs corresponding to a family that is hit, for a query, divided by the total number of PSSMs in the family can distinguish effectively the true positives from the false positives in the multiple profiles search approach.     

GPCRDB information system for G protein-coupled receptors

The GPCRDB is a molecular class-specific information system that collects, combines, validates and disseminates heterogeneous data on G protein-coupled receptors (GPCRs). The database stores data on sequences, ligand binding constants and mutations. The system also provides computationally derived data such as sequence alignments, homology models, and a series of query and visualization tools. The GPCRDB is updated automatically once every 4-5 months and is freely accessible at http://www.gpcr.org/7tm/.     

Storing biological sequence databases in relational form

SUMMARY: We have created a set of applications using Perl and Java in combination with XML technology to install biological sequence databases into an Oracle RDBMS. An easy-to-use interface using Java has been created for database query and other tools developed to integrate with our in-house bioinformatics applications. AVAILIBILITY: The database schema, DTD file, and source codes are available from the authors via email. CONTACT: guochun_ xie@merck. com     

PfamAlyzer: domain-centric homology search

PfamAlyzer is a Java applet that enables exploration of Pfam domain architectures using a user-friendly graphical interface. It can search the UniProt protein database for a domain pattern. Domain patterns similar to the query are presented graphically by PfamAlyzer either in a ranked list or pinned to the tree of life. Such domain-centric homology search can assist identification of distant homologs with shared domain architecture. AVAILABILITY: PfamAlyzer has been integrated with the Pfam database and can be accessed at http://pfam.cgb.ki.se/pfamalyzer.     

Using multiple alignments to improve seeded local alignment algorithms

Multiple alignments among genomes are becoming increasingly prevalent. This trend motivates the development of tools for efficient homology search between a query sequence and a database of multiple alignments. In this paper, we present an algorithm that uses the information implicit in a multiple alignment to dynamically build an index that is weighted most heavily towards the promising regions of the multiple alignment. We have implemented Typhon, a local alignment tool that incorporates our indexing algorithm, which our test results show to be more sensitive than algorithms that index only a sequence. This suggests that when applied on a whole-genome scale, Typhon should provide improved homology searches in time comparable to existing algorithms.     

Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions

Knowledge discovery from the exponentially growing body of structurally characterised protein-ligand complexes as a source of information in structure-based drug design is a major challenge in contemporary drug research. Given the need for powerful data retrieval, integration and analysis tools, Relibase was developed as a database system particularly designed to handle protein-ligand related problems and tasks. Here, we describe the design and functionality of the Relibase core database system. Features of Relibase include, e.g. the detailed analysis of superimposed ligand binding sites, ligand similarity and substructure searches, and 3D searches for protein-ligand and protein-protein interaction patterns. The broad range of functions provided in Relibase and its high level of data integration, along with its flexible and intuitive interface, makes Relibase an invaluable data mining tool which can significantly enhance the drug development process. An example, illustrating a 3D query for quarternary ligand nitrogen atoms interacting with aromatic ring systems in proteins, a pattern found in pharmaceutically relevant target proteins such as, e.g. acetylcholine-esterase, is discussed.     

Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima

We have determined the crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima, TM0651 (gi 4981173), at 2.2 A resolution by selenomethionine single-wavelength anomalous diffraction (SAD) techniques. TM0651 is a member of the haloacid dehalogenase (HAD) superfamily, with sequence homology to trehalose-6-phosphate phosphatase and sucrose-6(F)-phosphate phosphohydrolase. Selenomethionine labeled TM0651 crystallized in space group C2 with three monomers per asymmetric unit. Each monomer has approximate dimensions of 65 x 40 x 35 A(3), and contains two domains: a domain of known hydrolase fold characteristic of the HAD family, and a domain with a new tertiary fold consisting of a six-stranded beta-sheet surrounded by four alpha-helices. There is one disulfide bond between residues Cys35 and Cys265 in each monomer. One magnesium ion and one sulfate ion are bound in the active site. The superposition of active site residues with other HAD family members indicates that TM0651 is very likely a phosphatase that acts through the formation of a phosphoaspartate intermediate, which is supported by both NMR titration data and a biochemical assay. Structural and functional database searches and the presence of many aromatic residues in the interface of the two domains suggest the substrate of TM0651 is a carbohydrate molecule. From the crystal structure and NMR data, the protein likely undergoes a conformational change upon substrate binding.     

Assessment of a rigorous transitive profile based search method to detect remotely similar proteins

Profile-based sequence search procedures are commonly employed to detect remote relationships between proteins. We provide an assessment of a Cascade PSI-BLAST protocol that rigorously employs intermediate sequences in detecting remote relationships between proteins. In this approach we detect using PSI-BLAST, which involves multiple rounds of iteration, an initial set of homologues for a protein in a 'first generation' search by querying a database. We propagate a 'second generation' search in the database, involving multiple runs of PSI-BLAST using each of the homologues identified in the previous generation as queries to recognize homologues not detected earlier. This non-directed search process can be viewed as an iteration of iterations that is continued to detect further homologues until no new hits are detectable. We present an assessment of the coverage of this 'cascaded' intermediate sequence search on diverse folds and find that searches for up to three generations detect most known homologues of a query. Our assessments show that this approach appears to perform better than the traditional use of PSI-BLAST by detecting 15% more relationships within a family and 35% more relationships within a superfamily. We show that such searches can be performed on generalized sequence databases and non-trivial relationships between proteins can be detected effectively. Such a propagation of searches maximizes the chances of detecting distant homologies by effectively scanning protein "fold space".     

Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: application

Based on a study involving structural comparisons of proteins sharing 25% or less sequence identity, three rounds of Psi-BLAST appear capable of identifying remote evolutionary homologs with greater than 95% confidence provided that more than 50% of the query sequence can be aligned with the target sequence. Since it seems that more than 80% of all homologous protein pairs may be characterized by a lack of significant sequence similarity, the experimental biologist is often confronted with a lack of guidance from conventional homology searches involving pair-wise sequence comparisons. The ability to disregard levels of sequence identity and expect value in Psi-BLAST if at least 50% of the query sequence has been aligned allows for generation of new hypotheses by consideration of matches that are conventionally disregarded. In one example, we suggest a possible evolutionary linkage between the cupredoxin and immunoglobulin fold families. A thermostable hypothetical protein of unknown function may be a circularly permuted homolog to phosphotriesterase, an enzyme capable of detoxifying organophosphate nerve agents. In a third example, the amino acid sequence of another hypothetical protein of unknown function reveals the ATP binding-site, metal binding site, and catalytic sidechain consistent with kinase activity of unknown specificity. This approach significantly expands the utility of existing sequence data to define the primary structure degeneracy of binding sites for substrates, cofactors and other proteins.     

基因重组与基因合成实验设计软件系统的建立

本文报导了用于基因重组与基因合成实验设计的软件系统的建立.此系统由30个功能模块组成,为研究者提供了包括在DNA分子上寻找限制性内切酶位点、核酸分子片段之间同源性比较,基因化学合成的实验设计、特定顺序分析引物及核酸杂交探针的设计、阅读框的查找等功能.此外,本系统可以对外来数据库的资料进行援引和进一步分析,为分子生物学的研究提供有价值的信息.     

Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes

BLAST (Basic Local Alignment Search Tool) searches against DNA and protein sequence databases have become an indispensable tool for biomedical research. The proliferation of the genome sequencing projects is steadily increasing the fraction of genome-derived sequences in the public databases and their importance as a public resource. We report here the availability of Genomic BLAST, a novel graphical tool for simplifying BLAST searches against complete and unfinished genome sequences. This tool allows the user to compare the query sequence against a virtual database of DNA and/or protein sequences from a selected group of organisms with finished or unfinished genomes. The organisms for such a database can be selected using either a graphic taxonomy-based tree or an alphabetical list of organism-specific sequences. The first option is designed to help explore the evolutionary relationships among organisms within a certain taxonomy group when performing BLAST searches. The use of an alphabetical list allows the user to perform a more elaborate set of selections, assembling any given number of organism-specific databases from unfinished or complete genomes. This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes.     

Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches

Background

BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific score matrix (PSSM) for searching the database in round i?+?1. Biegert and S?ding developed Context-sensitive BLAST (CS-BLAST), which combines information from searching the sequence database with information derived from a library of short protein profiles to achieve better homology detection than PSI-BLAST, which builds its PSSMs from scratch.

Results

We describe a new method, called domain enhanced lookup time accelerated BLAST (DELTA-BLAST), which searches a database of pre-constructed PSSMs before searching a protein-sequence database, to yield better homology detection. For its PSSMs, DELTA-BLAST employs a subset of NCBI??s Conserved Domain Database (CDD). On a test set derived from ASTRAL, with one round of searching, DELTA-BLAST achieves a ROC₅₀₀₀ of 0.270 vs. 0.116 for CS-BLAST. The performance advantage diminishes in iterated searches, but DELTA-BLAST continues to achieve better ROC scores than CS-BLAST.

Conclusions

DELTA-BLAST is a useful program for the detection of remote protein homologs. It is available under the ??Protein BLAST?? link at http://blast.ncbi.nlm.nih.gov.

Reviewers

This article was reviewed by Arcady Mushegian, Nick V. Grishin, and Frank Eisenhaber.     

Solution structure of the first SH3 domain of human vinexin and its interaction with vinculin peptides

Solution structure of the first Src homology (SH) 3 domain of human vinexin (V_SH3_1) was determined using nuclear magnetic resonance (NMR) method and revealed that it was a canonical SH3 domain, which has a typical beta-beta-beta-beta-alpha-beta fold. Using chemical shift perturbation and surface plasmon resonance experiments, we studied the binding properties of the SH3 domain with two different peptides from vinculin hinge regions: P856 and P868. The observations illustrated slightly different affinities of the two peptides binding to V_SH3_1. The interaction between P868 and V_SH3_1 belonged to intermediate exchange with a modest binding affinity, while the interaction between P856 and V_SH3_1 had a low binding affinity. The structure and ligand-binding interface of V_SH3_1 provide a structural basis for the further functional study of this important molecule.     

A protein short motif search tool using amino acid sequence and their secondary structure assignment

We present the development of a web server, a protein short motif search tool that allows users to simultaneously search for a protein sequence motif and its secondary structure assignments. The web server is able to query very short motifs searches against PDB structural data from the RCSB Protein Databank, with the users defining the type of secondary structures of the amino acids in the sequence motif. The output utilises 3D visualisation ability that highlights the position of the motif in the structure and on the corresponding sequence. Researchers can easily observe the locations and conformation of multiple motifs among the results. Protein short motif search also has an application programming interface (API) for interfacing with other bioinformatics tools. AVAILABILITY: The database is available for free at http://birg3.fbb.utm.my/proteinsms.     

Sequence clustering strategies improve remote homology recognitions while reducing search times

Sequence databases are rapidly growing, thereby increasing the coverage of protein sequence space, but this coverage is uneven because most sequencing efforts have concentrated on a small number of organisms. The resulting granularity of sequence space creates many problems for profile-based sequence comparison programs. In this paper, we suggest several strategies that address these problems, and at the same time speed up the searches for homologous proteins and improve the ability of profile methods to recognize distant homologies. One of our strategies combines database clustering, which removes highly redundant sequence, and a two-step PSI-BLAST (PDB-BLAST), which separates sequence spaces of profile composition and space of homology searching. The combination of these strategies improves distant homology recognitions by more than 100%, while using only 10% of the CPU time of the standard PSI-BLAST search. Another method, intermediate profile searches, allows for the exploration of additional search directions that are normally dominated by large protein sub-families within very diverse families. All methods are evaluated with a large fold-recognition benchmark.