bluuebunny/crossref_metadata_2025_split huggingface dataset:
FluxAnalyzer: exploring structure, pathways, and
flux distributions in metabolic networks on interactive flux maps
Authors: Klamt Steffen , Stelling Jörg , Ginkel Martin , Gilles Ernst Dieter 
Published: January 2003

Abstract
Motivation: The analysis of structure, pathways and flux distributions in metabolic networks has become an important approach for understanding the functionality of metabolic systems. The need of a user-friendly platform for stoichiometric modeling of metabolic networks in silico is evident.
Results: The FluxAnalyzer is a package for MATLAB® and facilitates integrated pathway and flux analysis for metabolic networks within a graphical user interface. Arbitrary metabolic network models can be composed by instances of four types of network elements. The abstract network model is linked with network graphics leading to interactive flux maps which allow for user input and display of calculation results within a network visualization. Therein, a large and powerful collection of tools and algorithms can be applied interactively including metabolic flux analysis, flux optimization, detection of topological features and pathway analysis by elementary flux modes or extreme pathways. The FluxAnalyzer has been applied and tested for complex networks with more than 500 000 elementary modes. Some aspects of the combinatorial complexity of pathway analysis in metabolic networks are discussed.
Availability: Upon request from the corresponding author. Free for academic users (license agreement). Special contracts are available for industrial corporations.
Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer.
Contact: klamt@mpi-magdeburg.mpg.de
* To whom correspondence should be addressed.
Reconstruction of metabolic networks from genome data and analysis
of their global structure for various organisms
Authors: Ma Hongwu , Zeng An-Ping 
Published: January 2003

Abstract
Motivation: Information from fully sequenced genomes makes it possible to reconstruct strain-specific global metabolic network for structural and functional studies. These networks are often very large and complex. To properly understand and analyze the global properties of metabolic networks, methods for rationally representing and quantitatively analyzing their structure are needed.
Results: In this work, the metabolic networks of 80 fully sequenced organisms are in silico reconstructed from genome data and an extensively revised bioreaction database. The networks are represented as directed graphs and analyzed by using the‘ breadth first searching algorithm to identify the shortest pathway (path length) between any pair of the metabolites. The average path length of the networks are then calculated and compared for all the organisms. Different from previous studies the connections through current metabolites and cofactors are deleted to make the path length analysis physiologically more meaningful. The distribution of the connection degree of these networks is shown to follow the power law, indicating that the overall structure of all the metabolic networks has the characteristics of a small world network. However, clear differences exist in the network structure of the three domains of organisms. Eukaryotes and archaea have a longer average path length than bacteria.
Availability: The reaction database in excel format and the programs in VBA (Visual Basic for Applications) are available upon request.
Supplementary Material: Bioinformatics Online.
Contact: aze@gbf.de; hwm@gbf.de
* To whom correspondence should be addressed.
A task framework for the web interface W2H
Authors: Ernst Peter , Glatting Karl-Heinz , Suhai Sándor 
Published: January 2003

Abstract
Summary: The W3H task framework allows the execution of compound jobs utilizing the description of work and data flows in a heterogeneous bioinformatics environment using meta-data information. By means of these descriptions, the task system can schedule the necessary execution of applications available in the environment, depending on rules specified in the meta-data. By integrating this task framework into the publicly available web interface W2H, similarly based on meta-data, web access and data management are immediately available for each task description. Authors of task descriptions can base their work on the underlying classes and objects to be able to describe dependency rules between previously independent applications. The result of a compound task is given as XML data that is translated according to XSLT data into web pages or plain text to report the result of the task to the user.
Availability: Within the HUSAR environment at DKFZ http://genome.dkfz-heidelberg.de/
Contact: P.Ernst@dkfz.de
* To whom correspondence should be addressed.
QuickLIMS: facilitating the data management for DNA-microarray fabrication
Authors: Kokocinski Felix , Wrobel Gunnar , Hahn Meinhard , Lichter Peter 
Published: January 2003

Abstract
Summary: QuickLIMS is a Microsoft Access-based laboratory information and management system, capable of processing all information for microarray production. The program’s operational flow is protocol-based, dynamically adapting to changes of the process. It interacts with the laboratory robot and with other database systems over the network, and it represents a complete solution for the management of the entire manufacturing process.
Availability and supplementary information: http://www.dkfz-heidelberg.de/kompl_genome/Other/QuickLims/index.html
Contact: f.kokocinski@dkfz.def.kokocinski@dkfz.de
* To whom correspondence should be addressed.
An efficient algorithm for minimal primer set selection
Authors: Hsieh Ming-Hua , Hsu Wei-Che , Chiu Sung-Kay , Tzeng Chi-Meng 
Published: January 2003

Abstract
Summary: We have developed U-PRIMER, a primer design program, to compute a minimal primer set (MPS) for any given set of DNA sequences. The U-PRIMER algorithm, which uses automatic variable fixing and automatic redundant constraint elimination to tackle the binary integer programming problem associated with the MPS selection problem. The program has been tested successfully with 32 adipocyte development-related genes and 9 TB-specific genes to obtain their respective MPSs.
Availability: A free copy of U-PRIMER implemented in C++ programming language is available from http://www.u-vision-biotech.com
Contact: cmtzeng@u-vision-biotech.com
* To whom correspondence should be addressed.
Efficient selective screening of haplotype tag SNPs
Authors: Ke Xiayi , Cardon Lon R. 
Published: January 2003

Abstract
Abstract: Haplotypes defined by common single nucleotide polymorphisms (SNPs) have important implications for mapping of disease genes and human traits. Often only a small subset of the SNPs is sufficient to capture the full haplotype information. Such subsets of markers are called haplotype tagging SNPs (htSNPs). Although htSNPs can be identified by eye, efficient computer algorithms and flexible interactive software tools are required for large datasets such as the human genome haplotype map. We describe a java-based program, SNPtagger, which screens for minimal sets of SNP markers to represent given haplotypes according to various user requirements. The program offers several options for inclusion/exclusion of specific markers and presents alternative panels for final selection.
Availability: The www-based program is available at http://www.well.ox.ac.uk/~xiayi/haplotype/index.html.
Contact: xiayi@well.ox.ac.uk
* To whom correspondence should be addressed.
Simulating haplotype blocks in the human genome
Authors: Posada David , Wiuf Carsten 
Published: January 2003

Abstract
Summary: A bioinformatic tool was written to simulate haplotypes and SNPs under a modified coalescent with recombination. The most important feature of this program is that it allows for the specification of non-homogeneous recombination rates, which results in the formation of the so-called ‘haplotype blocks’ of the human genome. The program also implements different mutation models and flexible demographic histories. The samples generated can be very useful to better understand the architecture of the human genome and to investigate its impact in association studies searching for disease genes.
Availability: The SNPsim package is available at http://www.evolgenics.com/software
Contact: dposada@evolgenics.com
* To whom correspondence should be addressed.
Pedstrip: extracting a maximal subset of available,
unrelated individuals from a pedigree
Authors: Martin Jeremy M.R. , Mackay lan J. , Rawlings Christopher J. 
Published: January 2003

Abstract
Summary: Certain types of genetic analysis are simplified by assembling a collection of unrelated individuals, e.g. case-control experiments. If a family study is being performed then it will be necessary to extract subsets of unrelated, available individuals from pedigress. Our program provides an optimal method for performing this task.
Availability: The software is available, free of charge, on request from Oxagen Ltd.
Contact: SD@oxagen.co.uk
Supplementary information: http://www.oxagen.co.uk
* To whom correspondence should be addressed.
AVA: visual analysis of gene expression microarray data
Authors: Zhou Yihua , Liu Jingdong 
Published: January 2003

Abstract
Summary: AVA (Array Visual Analyzer) is a Java program that provides a graphical environment for visualization and analysis of gene expression microarray data. Together with its interactive visualization tools and a variety of built-in data analysis and filtration methods, AVA effectively integrates microarray data normalization, quality assessment, and data mining into one application.
Availability: The software is freely available for academic users on request from the authors.
Contact: yihua-zhou2@monsanto.com
* To whom correspondence should be addressed.
Matrix2png: a utility for visualizing matrix data
Authors: Pavlidis Paul , Noble William Stafford 
Published: January 2003

Abstract
We describe a simple software tool, ‘matrix2png’, for creating color images of matrix data. Originally designed with the display of microarray data sets in mind, it is a general tool that can be used to make simple visualizations of matrices for use in figures, web pages, slide presentations and the like. It can also be used to generate images ‘on the fly’ in web applications. Both continuous-valued and discrete-valued (categorical) data sets can be displayed. Many options are available to the user, including the colors used, the display of row and column labels, and scale bars. In this note we describe some of matrix2png’s features and describe some places it has been useful in the authors’ work.
Availability: A simple web interface is available, and Unix binaries are available from http://microarray.cpmc.columbia.edu/matrix2png. Source code is available on request.
Contact: pp175@columbia.edu
* To whom correspondence should be addressed at Russ Berrie Pavilion Room 121, 1150 St. Nicholas Ave, New York, NY 10025, USA.
RnaViz 2: an improved representation of RNA secondary structure
Authors: De Rijk Peter , Wuyts Jan , De Wachter Rupert 
Published: January 2003

Abstract
Summary: RnaViz has been developed to easily create nice, publication quality drawings of RNA secondary structure. RnaViz 2 supports CT, DCSE, and RNAML input formats and improves on many aspects of the first version, notably portability and structure annotation. RnaViz is written using a hybrid programming approach combining pieces written in C and in the scripting language Tcl/Tk, making the program very portable and extensible.
Availability: Source code, binaries for Linux and MS Windows, and additional documentation are available athttp://rrna.uia.ac.be/rnaviz/
Contact: derijkp@uia.ua.ac.be
* To whom correspondence should be addressed.
TopDraw: a sketchpad for protein structure topology cartoons
Authors: Bond Charles S. 
Published: January 2003

Abstract
Summary: Protein topology cartoons are a representation of structural data commonly used by structural biologists to illustrate the relationship between one-dimensional sequence and three-dimensional structural data in a convenient two-dimensional format. TopDraw is a simple, freely available TCL/Tk based drawing program designed specifically for the production of publication quality topology cartoons in a style commonly presented by structural biologists.
Availability: TopDraw is freely available under the terms of the GNU General Public License. It can be downloaded from http://stein.bioch.dundee.ac.uk/~charlie/scripts/topdraw.html.
Contact: C.S.Bond@dundee.ac.uk
ARIA: automated NOE assignment and NMR structure
calculation
Authors: Linge Jens P. , Habeck Michael , Rieping Wolfgang , Nilges Michael 
Published: January 2003

Abstract
Motivation: In the light of several ongoing structural genomics projects, faster and more reliable methods for structure calculation from NMR data are in great demand. The major bottleneck in the determination of solution NMR structures is the assignment of NOE peaks (nuclear Overhauser effect). Due to the high complexity of the assignment problem, most NOEs cannot be directly converted into unambiguous inter-proton distance restraints.
Results: We present version 1.2 of our program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of NOE data and NMR structure calculation. We summarize recent progress in correcting for spin diffusion with a relaxation matrix approach, representing non-bonded interactions in the force field and refining final structures in explicit solvent. We also discuss book-keeping, data exchange with spectra assignment programs and deposition of the analysed experimental data to the databases.
Availability: ARIA 1.2 is available from: http://www.pasteur.fr/recherche/unites/Binfs/aria/.
Supplementary information: XML DTDs (for chemical shifts and NOE crosspeaks), Python scripts for the conversion of various NMR data formats and the results of example calculations using data from the S. cerevisiae HRDC domain are available from: http://www.pasteur.fr/recherche/unites/Binfs/aria/.
Contact: linge@pasteur.fr
Visualization and analysis of protein interactions
Authors: Ju Byong-Hyon , Park Byungkyu , Park Jong H. , Han Kyungsook 
Published: January 2003

Abstract
Summary: We have developed a new program called InterViewer for drawing large-scale protein interaction networks in three-dimensional space. Unique features of InterViewer include (1) it is much faster than other recent implementations of drawing algorithms; (2) it can be used not only for visualizing protein interactions but also for analyzing them interactively; and (3) it provides an integrated framework for querying protein interaction databases and directly visualizes the query results.
Availability: http://wilab.inha.ac.kr/protein/
Contact: khan@inha.ac.kr
* To whom correspondence should be addressed.
Insights into binding cooperativity of MATa1/MATα2 from the crystal structure of a MATa1 homeodomain‐maltose binding protein chimera
Authors: Ke Ailong , Wolberger Cynthia 
Published: January 2003

AbstractThe Yeast MATa1 and MATα2 are homeodomain proteins that bind DNA cooperatively to repress transcription of cell type specific genes. The DNA affinity and specificity of MATa1 in the absence of MATα2, however, is very low. MATa1 is converted to a higher affinity DNA‐binding protein by its interaction with the C‐terminal tail of MATα2. To understand why MATa1 binds DNA weakly by itself, and how the MATα2 tail affects the affinity of MATa1 for DNA, we determined the crystal structure of a maltose‐binding protein (MBP)‐a1 chimera whose DNA binding behavior is similar to MATa1. The overall MATa1 conformation in the MBP‐a1 structure, which was determined in the absence of α2 and DNA, is similar to that in the a1/α2/DNA structure. The sole difference is in the C‐terminal portion of the DNA recognition helix of MATa1, which is flexible in the present structure. However, these residues are not in a location likely to be affected by binding of the MATα2 tail. The results argue against conformational changes in a1 induced by the tail of MATα2, suggesting instead that the MATα2 tail energetically couples the DNA binding of MATα2 and MATa1.
Accurate and automated classification of protein secondary structure with PsiCSI
Authors: Hung Ling‐Hong , Samudrala Ram 
Published: January 2003

AbstractPsiCSI is a highly accurate and automated method of assigning secondary structure from NMR data, which is a useful intermediate step in the determination of tertiary structures. The method combines information from chemical shifts and protein sequence using three layers of neural networks. Training and testing was performed on a suite of 92 proteins (9437 residues) with known secondary and tertiary structure. Using a stringent cross‐validation procedure in which the target and homologous proteins were removed from the databases used for training the neural networks, an average 89% Q3 accuracy (per residue) was observed. This is an increase of 6.2% and 5.5% (representing 36% and 33% fewer errors) over methods that use chemical shifts (CSI) or sequence information (Psipred) alone. In addition, PsiCSI improves upon the translation of chemical shift information to secondary structure (Q3 = 87.4%) and is able to use sequence information as an effective substitute for sparse NMR data (Q3 = 86.9% without 13C shifts and Q3 = 86.8% with only Hα shifts available). Finally, errors made by PsiCSI almost exclusively involve the interchange of helix or strand with coil and not helix with strand (<2.5 occurrences per 10000 residues). The automation, increased accuracy, absence of gross errors, and robustness with regards to sparse data make PsiCSI ideal for high‐throughput applications, and should improve the effectiveness of hybrid NMR/de novo structure determination methods. A Web server is available for users to submit data and have the assignment returned.
Stabilization of a pH‐sensitive apoptosis‐linked coiled coil through single point mutations
Authors: Dutta Kaushik , Engler Frank A. , Cotton Levaughn , Alexandrov Andrei , Bedi Gurrinder S. , Colquhoun Jennifer , Pascal Steven M. 
Published: January 2003

AbstractThe apoptosis‐associated Par‐4 protein has been implicated in cancers of the prostate, colon, and kidney, and in Alzheimer's and Huntington's diseases, among other neurodegenerative disorders. Previously, we have shown that a peptide from the Par‐4 C‐terminus, which is responsible for Par‐4 self‐association as well as interaction with all currently identified effector molecules, is natively unfolded at neutral pH, but forms a tightly associated coiled coil at acidic pH and low temperature. Here, we have alternately mutated the two acidic residues predicted to participate in repulsive electrostatic interactions at the coiled coil interhelical interface. Analysis of circular dichroism spectra reveals that a dramatic alteration of the folding/unfolding equilibrium of this peptide can be effected through directed‐point mutagenesis, confirming that the two acidic residues are indeed key to the pH‐dependent folding behavior of the Par‐4 coiled coil, and further suggesting that alleviation of charge repulsion through exposure to either a low pH microenvironment or an electrostatically complementary environment may be necessary for efficient folding of the Par‐4 C‐terminus.
Non‐animal origin of animal thioredoxin reductases: Implications for selenocysteine evolution and evolution of protein function through carboxy‐terminal extensions
Authors: Novoselov Sergey V. , Gladyshev Vadim N. 
Published: January 2003

AbstractThioredoxin reductase (TR) and thioredoxin constitute a major cellular redox system present in all organisms. In contrast to a single form of thioredoxin, there are two TR types: One (bacterial type or small TR) is present in bacteria, archaea, plants, and most unicellular eukaryotes, whereas the second (animal or large TR) is only found in animals and typically contains a carboxy‐terminal penultimate selenocysteine encoded by TGA. Surprisingly, we detected sequences of large TRs in various unicellular eukaryotes. Moreover, green algae Chlamydomonas reinhardtii had both small and large TRs, with the latter being a selenoprotein, but no examples of horizontal gene transfer from animals to the green algae could be detected. In addition, phylogenetic analyses revealed that large TRs formed a subgroup of lower eukaryotic glutathione reductases (GRs). The data suggest that the large TR evolved in a lower eukaryote capable of selenocysteine insertion rather than in an animal. The enzyme appeared to evolve by a carboxy‐terminal extension of GR such that the resulting carboxy‐terminal glutathionelike peptide became an intramolecular substrate for GR and a reductant for thioredoxin. Subsequently, small TRs were lost in an organism that gave rise to animals, large TRs were lost in plants and fungi, and selenocysteine/cysteine replacements took place in some large TRs. Our data implicate carboxy‐terminal extension of proteins as a general mechanism of evolution of new protein function.
NMR solution structure of the activation domain of human procarboxypeptidase A2
Authors: Jiménez M. Angeles , Villegas Virtudes , Santoro Jorge , Serrano Luis , Vendrell Josep , Avilés Francesc X. , Rico Manuel 
Published: January 2003

AbstractThe activation domain of human procarboxypeptidase A2, ADA2h, is an 81‐residue globular domain released during the proteolytic activation of the proenzyme. The role of this and other similar domains as assistants of the correct folding of the enzyme is not fully understood. The folding pathway of ADA2h was characterized previously, and it was also observed that under certain conditions it may convert into amyloid fibrils in vitro. To gain insight into these processes, a detailed description of its three‐dimensional structure in aqueous solution is required so that eventual changes could be properly monitored. A complete assignment of the 1H and 15N resonances of ADA2h was performed, and the solution structure, as derived from a set of 1688 nonredundant constraints, is very well defined (pairwise backbone RMSD = 0.67 ± 0.17 Å for residues 10–80). The structure is composed of two antiparallel α‐helices comprising residues 19–32 and 58–69 packed on the same side of a three‐stranded β‐sheet spanning residues 10–15, 50–55, and 73–75. The global fold for the isolated human A2 activation domain is very similar to that of porcine carboxypeptidase B, as well as to the structure of the domain in the crystal of the intact human proenzyme. The observed structural differences relative to the intact human proenzyme are located at the interface between the activation domain and the enzyme and can be related with the activation mechanism. The backbone amide proton exchange behavior of ADA2h was also examined. The global free energy of unfolding obtained from exchange data of the most protected amide protons at pH 7.0 and 298K is 4.9 ± 0.3 kcal.mole−1, in good agreement with the values determined by thermal or denaturant unfolding studies.