bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local structure-based sequence profile database for local
and global protein structure predictions
Authors: Yang An-Suei , Wang Lu-yong 
Published: December 2002

Abstract
Motivation: A large body of evidence suggests that protein structural information is frequently encoded in local sequences—sequence–structure relationships derived from local structure/sequence analyses could significantly enhance the capacities of protein structure prediction methods. In this paper, the prediction capacity of a database (LSBSP2) that organizes local sequence–structure relationships encoded in local structures with two consecutive secondary structure elements is tested with two computational procedures for protein structure prediction. The goal is twofold: to test the folding hypothesis that local structures are determined by local sequences, and to enhance our capacity in predicting protein structures from their amino acid sequences.
Results: The LSBSP2 database contains a large set of sequence profiles derived from exhaustive pair-wise structural alignments for local structures with two consecutive secondary structure elements. One computational procedure makes use of the PSI-BLAST alignment program to predict local structures for testing sequence fragments by matching the testing sequence fragments onto the sequence profiles in the LSBSP2 database. The results show that 54% of the test sequence fragments were predicted with local structures that match closely with their native local structures. The other computational procedure is a filter system that is capable of removing false positives as possible from a set of PSI-BLAST hits. An assessment with a large set of non-redundant protein structures shows that the PSI-BLAST + filter system improves the prediction specificity by up to two-fold over the prediction specificity of the PSI-BLAST program for distantly related protein pairs. Tests with the two computational procedures above demonstrate that local sequence–structure relationships can indeed enhance our capacity in protein structure prediction. The results also indicate that local sequences encoded with strong local structure propensities play an important role in determining the native state folding topology.
Availability: All the computational and assessment procedures have been implemented in the integrated computational system PrISM.1 (Protein Informatics System for Modeling). The system and associated databases for LINUX systems can be downloaded from the website:www.columbia.edu/~ay1/
Contact: ay1@columbia.edu
* To whom correspondence should be addressed.
Structure–dependent sequence alignment for remotely
related proteins
Authors: Yang An-Suei 
Published: December 2002

Abstract
Motivation: The quality of a model structure derived from a comparative modeling procedure is dictated by the accuracy of the predicted sequence–template alignment. As the sequence–template pairs are increasingly remote in sequence relationship, the prediction of the sequence–template alignments becomes increasingly problematic with sequence alignment methods. Structural information of the template, used in connection with the sequence relationship of the sequence–template pair, could significantly improve the accuracy of the sequence–template alignment. In this paper, we describe a sequence–template alignment method that integrates sequence and structural information to enhance the accuracy of sequence–template alignments for distantly related protein pairs.
Results: The structure-dependent sequence alignment (SDSA) procedure was optimized for coverage and accuracy on a training set of 412 protein pairs; the structures for each of the training pairs are similar (RMSD&lt;∼4Å) but the sequence relationship is undetectable (average pair-wise sequence identity = 8%). The optimized SDSA procedure was then applied to extend PSI-BLAST local alignments by calculating the global alignments under the constraint of the residue pairs in the local alignments. This composite alignment procedure was assessed with a testing set of 1421 protein pairs, of which the pair-wise structures are similar (RMSD&lt;∼4Å) but the sequences are marginally related at best in each pair (average pair-wise sequence identity = 13%). The assessment showed that the composite alignment procedure predicted more aligned residues pairs with an average of 27% increase in correctly aligned residues over the standard PSI-BLAST alignments for the protein pairs in the testing set.
Availability: All the computational and assessment procedures have been implemented in the integrated computational system PrISM.1 (Protein Informatics System for Modeling). The system and associated databases for LINUX systems can be downloaded from the website: http://www.columbia.edu/~ay1/
Contact: ay1@columbia.edu
PFDB: a generic protein family database integrating the CATH domain
structure database with sequence based protein family resources
Authors: Shepherd Adrian J. , Martin Nigel J. , Johnson Roger G. , Kellam Paul , Orengo Christine A. 
Published: December 2002

Abstract
Motivation: The PFDB (Protein Family Database) is a new database designed to integrate protein family-related data with relevant functional and genomic data. It currently manages biological data for three projects—the CATH protein domain database (Orengo et al., 1997; Pearl et al., 2001), the VIDA virus domains database (Albà et al., 2001) and the Gene3D database (Buchan et al., 2001). The PFDB has been designed to accommodate protein families identified by a variety of sequence based or structure based protocols and provides a generic resource for biological research by enabling mapping between different protein families and diverse biochemical and genetic data, including complete genomes.
Results: A characteristic feature of the PFDB is that it has a number of meta-level entities (for example aggregation, collection and inclusion) represented as base tables in the final design. The explicit representation of relationships at the meta-level has a number of advantages, including flexibility—both in terms of the range of queries that can be formulated and the ability to integrate new biological entities within the existing design. A potential drawback with this approach—poor performance caused by the number of joins across meta-level tables—is avoided by implementing the PFDB with materialized views using the mature relational database technology of Oracle 8i. The resultant database is both fast and flexible.
This paper presents the principles on which the database has been designed and implemented, and describes the current status of the database and query facilities supported.
Availability: http://bsmsn01.biochem.ucl.ac.uk/
* To whom correspondence should be addressed.
A hierarchical approach to aligning collinear regions of genomes
Authors: Roytberg Mikhail A. , Ogurtsov Aleksey Y. , Shabalina Svetlana A. , Kondrashov Alexey S. 
Published: December 2002

Abstract
Motivation: As a first approximation, similarity between two long orthologous regions of genomes can be represented by a chain of local similarities. Within such a chain, pairs of successive similarities are collinear (non-conflicting), i.e. segments involved in the nth similarity precede in both sequences segments involved in the (n+1)th similarity. However, when all similarities between two long sequences are considered, usually there are many conflicts between them. Although some conflicts can be avoided by masking transposons or low-complexity sequences, selecting only those similarities that reflect orthology and, thus, belong to the evolutionarily true chain is not trivial.
Results: We propose a simple, hierarchical algorithm of finding the true chain of local similarities. Starting from similarities with low P-values, we resolve each pairwise conflict by deleting a similarity with a higher P-value. This greedy approach constructs a chain of similarities faster than when a chain optimal with respect to some global criterion is sought, and makes more sense biologically.
Availability: A software tool OWEN based on the proposed approach is described in the accompanying note and is freely available at ftp://ftp.ncbi.nih.gov/pub/kondrashov/owen
Contact: kondrashov@ncbi.nlm.nih.gov
Supplementary information: Algorithm Chain and examples of chains of local similarities are available at ftp://ftp.ncbi.nih.gov/pub/kondrashov/owen/extra
* To whom correspondence should be addressed.
SNPper: retrieval and analysis of human SNPs
Authors: Riva A. , Kohane I. S. 
Published: December 2002

Abstract
Motivation: Single Nucleotide Polymorphisms (SNPs) are an increasingly important tool for the study of the human genome. SNPs can be used as markers to create high-density genetic maps, as causal candidates for diseases, or to reconstruct the history of our genome. SNP-based studies rely on the availability of large numbers of validated, high-frequency SNPs whose position on the chromosomes is known with precision. Although large collections of SNPs exist in public databases, researchers need tools to effectively retrieve and manipulate them.
Results: We describe the implementation and usage of SNPper, a web-based application to automate the tasks of extracting SNPs from public databases, analyzing them and exporting them in formats suitable for subsequent use. Our application is oriented toward the needs of candidate-gene, whole-genome and fine-mapping studies, and provides several flexible ways to present and export the data. The application has been publicly available for over a year, and has received positive user feedback and high usage levels.
Availability: SNPper is freely available at http://snpper.chip.org/. Registration is optional and provides access to some advanced features.
Contact: Alberto.Riva@TCH.Harvard.edu
* To whom correspondence should be addressed.
Oligodb—interactive design of oligo DNA for transcription
profiling of human genes
Authors: Mrowka Ralf , Schuchhardt Johannes , Gille Christoph 
Published: December 2002

Abstract
Motivation: The increasing use of customized oligo-DNA-microarrays has created a demand for convenient design of oligo nucleotides. The oligo-nucleotides have to serve as specific templates in the hybridization reaction.
Results: We have devised a web-based system for interactive design of suitable oligos for transcription profiling experiments with user-defined parameters. Oligodb is based on predicted human gene transcripts from the ENSEMBL project. The web interface allows the user to retrieve oligos for human transcripts in a flexible manner. Criteria for selecting the oligos are low similarity to all other known human genes, the absence of stable secondary structures, the length of the oligo, and the absence of low complexity regions. Furthermore, the user may select oligos corresponding to the desired position in the 5’–3’ direction of the transcript, and based on the melting temperature. All data and results are tightly web-linked to the corresponding data entries of ENSEMBL project.
Availability: The working Oligodb system is to be found at http://oligodb.charite.de
Contact: ralf.mrowka@charite.de
* To whom correspondence should be addressed.
PCR designer for restriction analysis of various types of
sequence mutation
Authors: Ke Xiayi , Collins Andrew , Ye Shu 
Published: December 2002

Abstract
Summary: Restriction analysis is widely used to detect gene mutations such as insertions, deletions and single nucleotide polymorphisms (SNPs). Although such mutation sites sometimes present some natural restriction sites to differentiate the wild-type and mutant sequences, mismatches are often needed in order to create artificial restriction fragment length polymorphisms (RFLPs). In this report, a computer program is described that screens for suitable restriction enzymes, introducing mismatches where appropriate and when necessary, designs primers using the information of the selected restriction enzymes, their recognition sequence and locations as well as the information about the mismatches if any. The program, supported by a WWW web interface, is intended to be used online.
Availability: The computer software, with related documentation, is available at http://cedar.genetics.soton.ac.uk/public_html/primer.html
Contact: xiayi@well.ox.ac.uk
* To whom correspondence should be addressed.
Design of endonuclease restriction sites into primers for PCR cloning
Authors: Hou Jianghui 
Published: December 2002

Abstract
Summary: I present a software system PCRCLNG that facilitates the design of endonuclease restriction sites into the 5′-end of PCR primers. The product amplified using these primers can be directly cloned into vectors. The program estimates the annealing temperature for each primer and selects the primer pairs with comparable annealing temperature. Finally the software determines whether the PCR product can be cloned into the vector to generate in-frame gene fusion.
Availability: PCRCLNG is available for non-commercial users free of charge as a set of executables and source codes upon request from the author.
Contact: jianghui.hou@ed.ac.uk
RED: the analysis, management and dissemination of
expressed sequence tags
Authors: Everitt R. , Minnema S. E. , Wride M. A. , Koster C. S. , Hance J. E. , Mansergh F. C. , Rancourt D. E. 
Published: December 2002

Abstract
Summary: The Rancourt EST Database (RED) is a web-based system for the analysis, management, and dissemination of expressed sequence tags (ESTs). RED represents a flexible template DNA sequence database that can be easily manipulated to suit the needs of other laboratories undertaking mid-size sequencing projects.
Availability: http://www.ucalgary.ca/~rancourt
Contact: reveritt@ucalgary.ca
* To whom correspondence should be addressed.
1 Present address: Cardiff University, Biomedical Sciences Building, Museum Avenue, PO Box 911, Cardiff CF10 3US, Wales, UK.
GENECOUNTING: haplotype analysis with missing genotypes
Authors: Zhao Jing Hua , Lissarrague Sebastien , Essioux Laurent , Sham Pak Chung 
Published: December 2002

Abstract
Summary: A general algorithm is described for haplotype analysis of unrelated individuals with missing genotypes. It can handle problems involving multiple polymorphic markers with missing data.
Availability: GENECOUNTING is available fromhttp://www.iop.kcl.ac.uk/IoP/Departments/PsychMed/GEpiBSt/software.stm
Contact: j.zhao@public-health.ucl.ac.uk;p.sham@iop.kcl.ac.uk
* To whom correspondence should be addressed.
DNACompress: fast and effective DNA sequence compression
Authors: Chen Xin , Li Ming , Ma Bin , Tromp John 
Published: December 2002

Abstract
Summary: While achieving the best compression ratios for DNA sequences, our new DNACompress program significantly improves the running time of all previous DNA compression programs.
Availability: http://dna.cs.ucsb.edu/DNACompress
Contact: chxin@cs.ucsb.edumli@cs.ucsb.edu
* To whom correspondence should be addressed.
ADME-AP: a database of ADME associated proteins
Authors: Sun L. Z. , Ji Z. L. , Chen X. , Wang J. F. , Chen Y. Z. 
Published: December 2002

Abstract
Summary: Drug absorption, distribution, metabolism and excretion (ADME) often involve interaction of a drug with specific proteins. Knowledge about these ADME-associated proteins is important in facilitating the study of the molecular mechanism of disposition and individual response as well as therapeutic action of drugs. It is also useful in the development and testing of pharmacokinetics prediction tools. Several databases describing specific classes of ADME-associated proteins have appeared. A new database, ADME-associated proteins (ADME-AP), is introduced to provide comprehensive information about all classes of ADME-associated proteins described in the literature including physiological function of each protein, pharmacokinetic effect, ADME classification, direction and driving force of disposition, location and tissue distribution, substrates, synonyms, gene name and protein availability in other species. Cross-links to other databases are also provided to facilitate the access of information about the sequence, 3D structure, function, polymorphisms, genetic disorders, nomenclature, ligand binding properties and related literatures of each protein. ADME-AP currently contains entries for 321 proteins and 964 substrates.
Availability: http://xin.cz3.nus.edu.sg/group/admet/admet.asp
Contact: yzchen@cz3.nus.edu.sg
* To whom correspondence should be addressed.
PoPMuSiC, rationally designing point
mutations in protein structures
Authors: Kwasigroch J. M. , Gilis D. , Dehouck Y. , Rooman M. 
Published: December 2002

Abstract
Summary: PoPMuSiC is an efficient tool for rational computer-aided design of single-site mutations in proteins and peptides. Two types of queries can be submitted. The first option allows to estimate the changes in folding free energy for specific point mutations given by the user. In the second option, all possible point mutations in a given protein or protein region are performed and the most stabilizing or destabilizing mutations, or the neutral mutations with respect to thermodynamic stability, are selected. For each sequence position or secondary structure the deviation from the most stable sequence is moreover evaluated, which helps to identify the most suitable sites for the introduction of mutations.
Availability: http://babylone.ulb.ac.be/popmusic
Contact: jean.marc.kwasigroch@ulb.ac.be
* To whom correspondence should be addressed.
OWEN: aligning long collinear regions of genomes
Authors: Ogurtsov Aleksey Y. , Roytberg Mikhail A. , Shabalina Svetlana A. , Kondrashov Alexey S. 
Published: December 2002

Abstract
Summary: OWEN is an interactive tool for aligning two long DNA sequences that represents similarity between them by a chain of collinear local similarities. OWEN employs several methods for constructing and editing local similarities and for resolving conflicts between them. Alignments of sequences of lengths over 106 can often be produced in minutes. OWEN requires memory below 20 L, where L is the sum of lengths of the compared sequences.
Availability: Pre-compiled versions of OWEN for Windows, Linux for PC, SunOS for Sun, and Irix for SGI, user manual, and examples of alignments are freely available atftp://ftp.ncbi.nih.gov/pub/kondrashov/owen
Contact: ogurtsov@ncbi.nlm.nih.gov
* To whom correspondence should be addressed.
The GeneAround GO viewer
Authors: Tanoue Junko , Yoshikawa Masatoshi , Uemura Shunsuke 
Published: December 2002

Abstract
Summary: We have developed a system for visualizing the Gene Ontology™ hierarchy. The graphical browser interactively displays diagrams of the inheritance relationship for each term to help understand the meanings of terms when handling gene annotation data.
Availability: The GeneAround GO viewer is open to the public at http://db.aist-nara.ac.jp/genearound/
Contact: genearound@is.aist-nara.ac.jp
* To whom correspondence should be addressed at Information Technology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, JAPAN.
Oral Delivery ofMycobacterium bovisBCG in a Lipid Formulation Induces Resistance to Pulmonary Tuberculosis in Mice
Authors: Aldwell Frank E. , Tucker Ian G. , de Lisle Geoffrey W. , Buddle Bryce M. 
Published: December 2002

ABSTRACTA lipid-based formulation has been developed for oral delivery ofMycobacterium bovisbacille Calmette-Guérin (BCG) vaccine. The formulatedM. bovisBCG was fed to BALB/c mice to test for immune responses and protection againstM. bovisinfection. The immune responses included antigen-specific cytokine responses, spleen cell proliferation, and lymphocyte-mediated macrophage inhibition ofM. bovis. Oral delivery of formulatedM. bovisBCG to mice induced strong splenic gamma interferon levels and macrophage inhibition of virulentM. boviscompared with results with nonformulatedM. bovisBCG. Formulated oralM. bovisBCG significantly reduced the bacterial burden in the spleen and lungs of mice following aerosol challenge with virulentM. bovis. Our data suggest that oral delivery of formulatedM. bovisBCG is an effective means of inducing protective immune responses against tuberculosis. Lipid-based, orally delivered mycobacterial vaccines may be a safe and practical method of controlling tuberculosis in humans and animals.
Effective Induction of Acquired Resistance toListeria monocytogenesby Immunizing Mice with In Vivo-Infected Dendritic Cells
Authors: Sashinami Hiroshi , Nakane Akio , Iwakura Yoichiro , Sasaki Mutsuo 
Published: December 2002

ABSTRACTSplenic dendritic cells (DCs) obtained from mice at 48 h afterListeria monocytogenesinfection exhibited up-regulation of CD80 and produced higher titers of gamma interferon (IFN-γ) and interleukin-12 (IL-12) than did DCs obtained from uninfected mice. Mice immunized with DCs obtained from mice that had been infected withL. monocytogenes48 h before acquired host resistance to lethal infection withL. monocytogenesat 4 and 8 weeks. Immunization with DCs from heat-killedL. monocytogenesfailed to induce resistance. Acquired antilisterial resistance is specific, since the immunized mice could not be protected fromSalmonella entericaserovar Typhimurium infection. Infected DCs stimulated proliferation of naive CD4+and CD8+cells in vitro, suggesting that in vivo-infected DCs activate CD8+T cells, which are critical in acquired antilisterial resistance, as well as CD4+T cells. When wild-type mice were immunized with DCs from IFN-γ-deficient mice, they were protected against a lethalL. monocytogeneschallenge. In contrast, when mice were immunized with DCs from anti-IL-12 p40 monoclonal antibody-injected mice, they failed to gain acquired antilisterial resistance. These results suggest that DC-derived IL-12, but not IFN-γ, may play a critical role in induction of acquired antilisterial resistance. Our present results suggest that splenic DCs obtained from mice infected withL. monocytogenesin vivo may be an effective immunogen with which to induce antigen-specific immunity.
Pathogenicity and Immune Response Measured in Mice following Intranasal Challenge with EnterotoxigenicEscherichia coliStrains H10407 and B7A
Authors: Byrd Wyatt , Mog Steven R. , Cassels Frederick J. 
Published: December 2002

ABSTRACTThe pathogenicity and immunogenicity induced in BALB/c mice by intranasal (i.n.) inoculation of enterotoxigenicEscherichia coli(ETEC) strains H10407 (O78:H11:CFA/I:LT+:ST+) and B7A (O148:H28:CS6:LT+:ST+) (two ETEC strains previously used in human challenge trials) were studied. The i.n. inoculation of BALB/c mice with large doses of ETEC strains H10407 and B7A caused illness and death. The H10407 strain was found to be consistently more virulent than the B7A strain. Following i.n. challenge with nonlethal doses of H10407 and B7A, the bacteria were cleared from the lungs of the mice at a steady rate over a 2-week period. Macrophages and neutrophils were observed in the alveoli and bronchioles, and lymphocytes were observed in the septa, around vessels, and in the pleura of the lungs in mice challenged with H10407 and B7A. In mice i.n. challenged with H10407, serum immunoglobulin G (IgG) and IgM antibodies were measured at high titers to the CFA/I and O78 lipopolysaccharide (LPS) antigens. In mice i.n. challenged with B7A, low serum IgG antibody titers were detected against CS6, and low serum IgG and IgM antibody titers were detected against O148 LPS. The serum IgG and IgM antibody titers against the heat-labile enterotoxin were equivalent in the H10407- and B7A-challenged mice. The CFA/I and O78 LPS antigens gave mixed T-helper cell 1-T-helper cell 2 (Th1-Th2) responses in which the Th2 response was greater than the Th1 response (i.e., stimulated primarily an antibody response). These studies indicate that the i.n. challenge of BALB/c mice with ETEC strains may provide a useful animal model to better understand the immunogenicity and pathogenicity of ETEC and its virulence determinants. This model may also be useful in providing selection criteria for vaccine candidates for use in primate and human trials.