bluuebunny/crossref_metadata_2025_split huggingface dataset:
Equilibrium and kinetic folding of hen egg‐white lysozyme under acidic conditions
Authors: Sasahara Kenji , Demura Makoto , Nitta Katsutoshi 
Published: October 2002

AbstractThe equilibrium and kinetic folding of hen egg‐white lysozyme was studied by means of circular dichroism spectra in the far‐ and near‐ultraviolet (UV) regions at 25°C under the acidic pH conditions. In equilibrium condition at pH 2.2, hen lysozyme shows a single cooperative transition in the GdnCl‐induced unfolding experiment. However, in the GdnCl‐induced unfolding process at lower pH 0.9, a distinct intermediate state with molten globule characteristics was observed. The time‐dependent unfolding and refolding of the protein were induced by concentration jumps of the denaturant and measured by using stopped‐flow circular dichroism at pH 2.2. Immediately after the dilution of denaturant, the kinetics of refolding shows evidence of a major unresolved far‐UV CD change during the dead time (<10 ms) of the stopped‐flow experiment (burst phase). The observed refolding and unfolding curves were both fitted well to a single‐exponential function, and the rate constants obtained in the far‐ and near‐UV regions coincided with each other. The dependence on denaturant concentration of amplitudes of burst phase and both rate constants was modeled quantitatively by a sequential three‐state mechanism, U↔I↔N, in which the burst‐phase intermediate (I) in rapid equilibrium with the unfolded state (U) precedes the rate‐determining formation of the native state (N). The role of folding intermediate state of hen lysozyme was discussed. Proteins 2002;49:472–482. © 2002 Wiley‐Liss, Inc.
All‐atom fast protein folding simulations: The villin headpiece
Authors: Shen Min‐yi , Freed Karl F. 
Published: October 2002

AbstractWe provide a fast folding simulation using an all‐atom solute, implicit solvent method that eliminates the need for treating solvent degrees of freedom. The folding simulations for the 36‐residue villin headpiece exhibit close correspondence with the landmark all‐atom explicit solvent molecular dynamics simulations by Duan and Kollman (Duan & Kollman, Science 1998;282:740–744; Duan, Wang, & Kollman, Proc Natl Acad Sci USA 1998;95:9897–9902). Our implicit solvent approach uses only an entry‐level single CPU PC with comparable throughput (∼4 nsec/day) to the DK supercomputer simulation. The native state is shown to be stable. Our 200‐nsec folding trajectory agrees with the DK simulation in displaying a burst phase, a rapid initial shrinkage, a highly native‐like binding site structure, and more. Proteins 2002;49:439–445. © 2002 Wiley‐Liss, Inc.
FROST: A filter‐based fold recognition method
Authors: Marin Antoine , Pothier Joël , Zimmermann Karel , Gibrat Jean‐François 
Published: October 2002

AbstractTo assess the reliability of fold assignments to protein sequences, we developed a fold recognition method called FROST (Fold Recognition‐Oriented Search Tool) based on a series of filters and a database specifically designed as a benchmark for this new method under realistic conditions. This benchmark database consists of proteins for which there exists, at least, another protein with an extensively similar 3D structure in a database of representative 3D structures (i.e., more than 65% of the residues in both proteins can be structurally aligned). Because the testing of our method must be carried out under conditions similar to those of real fold recognition experiments, no protein pair with sequence similarity detectable using standard sequence comparison methods such as FASTA is included in the benchmark database. While using FROST, we achieved a coverage of 60% for a rate of error of 1%. To obtain a baseline for our method, we used PSI‐BLAST and 3D‐PSSM. Under the same conditions, for a 1% error rate, coverages for PSI‐BLAST and 3D‐PSSM were 33 and 56%, respectively. Proteins 2002;49:493–509. © 2002 Wiley‐Liss, Inc.
A new test set for validating predictions of protein–ligand interaction
Authors: Nissink J. Willem M. , Murray Chris , Hartshorn Mike , Verdonk Marcel L. , Cole Jason C. , Taylor Robin 
Published: October 2002

AbstractWe present a large test set of protein–ligand complexes for the purpose of validating algorithms that rely on the prediction of protein–ligand interactions. The set consists of 305 complexes with protonation states assigned by manual inspection. The following checks have been carried out to identify unsuitable entries in this set: (1) assessing the involvement of crystallographically related protein units in ligand binding; (2) identification of bad clashes between protein side chains and ligand; and (3) assessment of structural errors, and/or inconsistency of ligand placement with crystal structure electron density. In addition, the set has been pruned to assure diversity in terms of protein–ligand structures, and subsets are supplied for different protein‐structure resolution ranges. A classification of the set by protein type is available. As an illustration, validation results are shown for GOLD and SuperStar. GOLD is a program that performs flexible protein–ligand docking, and SuperStar is used for the prediction of favorable interaction sites in proteins. The new CCDC/Astex test set is freely available to the scientific community (http://www.ccdc.cam.ac.uk). Proteins 2002;49:457–471. © 2002 Wiley‐Liss, Inc.
Docking of non‐nucleoside inhibitors: Neotripterifordin and its derivatives to HIV‐1 reverse transcriptase
Authors: Zhou Zhigang , Madrid Marcela , Madura Jeffry D. 
Published: October 2002

AbstractThe docking of small molecules to proteins has played an important role in the understanding of drug/receptor interactions. An important drug/receptor interaction is between non‐nucleoside inhibitors of HIV‐1 RT and the non‐nucleoside binding pocket. We report the results of docking calculations in which we have docked known and proposed non‐nucleoside reverse transcriptase inhibitors to the type 1 virus. The proposed NNRTIs dock in a similar position and orientation as known inhibitors. In addition, we observe a linear correlation between the calculated interaction energy and EC50 for the inhibitors, suggesting that the docked structure orientation and the interaction energies are reasonable. Two hydrogen bonds between nevirapine and RT (3HVT and 1VRT) are observed and are reproduced across different docking schemes. Since we used two different HIV‐1 RT crystal structures (3HVT and 1VRT), which are at different levels of resolution (2.9 and 2.2 Å, respectively), we propose that structures with resolutions better than 3 Å can be used to produce reasonable docking results. Proteins 2002;49:529–542. © 2002 Wiley‐Liss, Inc.
Ligand specificity and ligand‐induced conformational change in gal repressor
Authors: Chatterjee Sumana , Ghosh Kajari , Dhar Amlanjyoti , Roy Siddhartha 
Published: October 2002

AbstractGal repressor (GalR) binds D‐galactose, which is responsible for lifting of repression of the gal operon. Proton T1 measurements of α‐ and β‐anomers of galactose as a function of gal repressor show preferential binding of the β‐anomer. The β‐anomer was isolated by high‐performance liquid chromatography and was shown to bind tightly to GalR. Calorimetry was used to determine enthalpy changes at several temperatures. Heat capacity change was found to be positive, indicating that a significant amount of hydrophobic surface area was exposed upon galactose binding. Bis‐ANS binding to GalR is significantly enhanced in the presence of a saturating amount of galactose, indicating additional exposure of hydrophobic surfaces. We propose that the galactose‐induced conformational change involves the opening of the two subdomains, which may disrupt protein–protein interactions responsible for repression. Proteins 2002;49:554–559. © 2002 Wiley‐Liss, Inc.
Stability scale and atomic solvation parameters extracted from 1023 mutation experiments
Authors: Zhou Hongyi , Zhou Yaoqi 
Published: October 2002

AbstractThe stability scale of 20 amino acid residues is derived from a database of 1023 mutation experiments on 35 proteins. The resulting scale of hydrophobic residues has an excellent correlation with the octanol‐to‐water transfer free energy corrected with an additional Flory–Huggins molar‐volume term (correlation coefficient r = 0.95, slope = 1.05, and a near zero intercept). Thus, hydrophobic contribution to folding stability is characterized remarkably well by transfer experiments. However, no corresponding correlation is found for hydrophilic residues. Both the hydrophilic portion and the entire scale, however, correlate strongly with average burial accessible surface (r = 0.76 and 0.97, respectively). Such a strong correlation leads to a near uniform value of the atomic solvation parameters for atoms C, S, O/N, O−0.5, and N+0.5,1. All are in the range of 12–28 cal mol−1 Å−2, close to the original estimate of hydrophobic contribution of 25–30 cal mol−1 Å−2 to folding stability. Without any adjustable parameters, the new stability scale and new atomic solvation parameters yielded an accurate prediction of protein–protein binding free energy for a separate database of 21 protein–protein complexes (r = 0.80 and slope = 1.06, and r = 0.83 and slope = 0.93, respectively). Proteins 2002;49:483–492. © 2002 Wiley‐Liss, Inc.
Influence of induced fit in the interaction of Bacillus subtilis trp RNA‐binding attenuator protein and its RNA antiterminator target oligomer
Authors: Flynn Peter F. , Wendt Alice , Gollnick Paul 
Published: October 2002

AbstractIn the presence of excess tryptophan, tryptophan‐activated TRAP (trp RNA‐binding attenuator protein) binds to a specific target in the trp‐leader transcript, which induces the formation of a transcription terminator and transcription halts in the leader region. In the absence of tryptophan, TRAP does not bind RNA, an antiterminator forms, and the operon is expressed. Although the ternary complex involving TRAP (Bacillus stearothermophilus), tryptophan, and the RNA target has recently been crystallized, efforts to obtain structural data for the apo‐form of TRAP (in any species) have not been successful. We have used multidimensional/multinuclear nuclear magnetic resonance (NMR) spectroscopy to probe the structure–function relationship in the TRAP‐activated system, and have obtained high‐resolution multidimensional/multinuclear NMR spectra of TRAP in all three of its functional states: tryptophan‐free or apo‐TRAP, tryptophan‐activated TRAP, and tryptophan‐activated TRAP‐RNA ternary complex. Chemical shift perturbation analysis of the NMR data clarifies the interpretation of results obtained from previous crystal studies. Results presented herein demonstrate that tryptophan binding induces an essential structural change in TRAP that supports high‐affinity binding of the RNA target oligonucleotide. Proteins 2002;49:432–438. © 2002 Wiley‐Liss, Inc.
Kinase inhibitors and the case for CH…O hydrogen bonds in protein–ligand binding
Authors: Pierce Albert C. , Sandretto Kathryn L. , Bemis Guy W. 
Published: October 2002

AbstractAlthough the hydrogen bond is known to be an important mediator of intermolecular interactions, there has yet to be an analysis of the role of CH…O hydrogen bonds in protein–ligand complexes. In this work, we present evidence for such nonstandard hydrogen bonds from a survey of aromatic ligands in 184 kinase crystal structures and 358 high‐resolution structures from the Protein Data Bank. CH groups adjacent to the positively charged nitrogen of nicotinamide exhibit geometric preferences strongly suggestive of hydrogen bonding interactions, as do heterocyclic CH groups in kinase ligands, while other aromatic CH groups do not exhibit these characteristics. Ab initio calculations reveal a considerable range of CH…O hydrogen bonding potentials among different aromatic ring systems, with nicotinamide and heterocycles preferred in kinase inhibitors showing particularly favorable interactions. These results provide compelling evidence for the existence of CH…O hydrogen bonds in protein–ligand interactions, as well as information on the relative strength of various aromatic CH donors. Such knowledge will be of considerable value in protein modeling, ligand design, and structure–activity analysis. Proteins 2002;49:567–576. © 2002 Wiley‐Liss, Inc.
Implementation of a multiagent system for competitive environments on the WWW
Authors: Onjo Hiroyuki , Far Behrouz H. 
Published: October 2002

AbstractAgents have been receiving a lot of attention as software which behaves autonomously and efficiently on a network and supports human social interactions. Various agent systems have already been proposed. A conventional agent‐based system is based on the assumption that all interacting agents are trustworthy. In practice, however, there are many instances in which agents must compete in an environment in which the other agents cannot be trusted. Thus, in this paper the authors discuss the development of an electronic commerce system which uses agents that behave competitively. The agents in this system can determine autonomously the level of uncertainty in a transaction, then make decisions flexibly. In addition, the authors argue for the validity of their system using operational examples in which their system is used in various market scenarios. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 34–49, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10032
2D spreading associative neural network simultaneously recognizes object position and shape in 2D space
Authors: Nakamura Kiyomi , Kinoshita Noriki , Kanayama Hirokazu 
Published: October 2002

AbstractThe original “spreading associative neural network,” which imitates the spatial recognition system in the brain, not only recognizes the shape of an object irrespective of its position, but also recognizes its position irrespective of its shape in the input pattern when the object positional movement is limited to only one dimension. In the present study, in order to allow an object presentation in any 2D position on the plane, we propose a “2D spreading associative neural network” which spreads the input pattern in two dimensions. The proposed neural network not only recognizes the shape of the object in the 2D space irrespective of its position, but also recognizes its position irrespective of its shape in the input pattern. The position‐invariant shape recognition and the shape‐invariant positional recognition ability in 2D space are obtained across various kinds of objects—characters and human faces—at the same time. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(13): 11–23, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10171
Active perception and recognition learning system based on Actor‐Q architecture
Authors: Shibata Katsunari , Nishino Tetsuo , Okabe Yoichi 
Published: October 2002

AbstractThis paper proposes the Actor‐Q architecture, which is a combination of Q‐Learning and Actor‐Critic architecture, as well as the active perception and recognition learning system based on that architecture. In Actor‐Q architecture, the system output is divided into the “action,” which is a discrete value as intention, and the “motion,” which is a continuous‐valued vector. As the first step, the “action” is determined from Q‐values. If the “action” is accompanied with a “motion,” the “motion” is executed according to the corresponding Actor output. Q‐value is learned by Q‐learning, and Actor is trained with the Q‐value corresponding to that “action” on behalf of the Critic output. In this study, the action is defined as the decision of the sensor motion or the recognition of the respective pattern. Q‐value is assigned to each of those. When the sensor motion is selected, the sensor is moved according to the Actor output. When recognition is selected, the recognition result that the presented pattern is the one corresponding to the selected Q‐value is output. The Q‐value is learned, using the reinforcement signal representing the true/false of the result. Both Q‐value computing module and Actor are composed of neural networks, with the visual sensor signals as input. By this architecture, the following three problems of the conventional active perception and recognition learning system are dissolved. (1) The sensor can be trapped in a local maximum of the recognition evaluation. (2) It is necessary that the recognition output should be evaluated for each time‐step, and the reinforcement signal with a continuous value should be provided. (3) The system cannot decide by itself the timing to output the recognition result. The above effect was verified by some simulations, using the visual sensor with nonuniform sensor cells. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 12–22, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10207
Built‐in Self‐Test for crosstalk faults in a digital VLSI
Authors: Shimizu Kazuya , Itazaki Noriyoshi , Kinoshita Kozo 
Published: October 2002

AbstractAccompanying high‐integration and high‐speed implementation of VLSI in recent years, new faults which cannot be classified in the category of conventional fault models have become a problem. Among these new faults, we will deal with crosstalk faults in this paper. Because of excitation and propagation of the crosstalk faults in the detection of these faults, two successive test vectors are required and thus their generation is difficult. Moreover, it is necessary in the sequential circuit to consider the problem of timing such as gate delay time and FF setup time in the circuit. For that reason, it has been difficult to realize a high fault coverage in the test vector generation methods proposed so far. To solve these problems, we will newly propose in this paper a Built‐In Self‐Test (BIST) method which can detect the crosstalk faults. This method can be realized by a relatively small area overhead; moreover, by adopting a circuit configuration during simulation which is different from the one during test, the simulation time is shortened. In this way, testing of large‐scale circuits has been made possible. We have performed an evaluation on the fault coverage for several benchmark circuits and shown that this method is effective for crosstalk faults. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(13): 35–47, 2002; Published online in Wiley InterScience (www. interscience.wiley.com). DOI 10.1002/scj.1171
High‐accuracy shape decomposition based on mathematical morphology in discrete circle space
Authors: Tong Weiqing , Tatsumi Shoji 
Published: October 2002

AbstractIn this paper, by improving the existing morphological shape decomposition method, we will propose a morphological shape decomposition which uses high‐accuracy circle‐structuring elements and is capable of completely describing the original shape. Moreover, the amount of calculation time for shape decomposition is determined, and it is found that both methods require the same calculation timeO(M4/3) (M2is the area of the object figure). Furthermore, from the viewpoints of shape description error rate and description data quantity, the proposed method is confirmed to be superior to the existing method in the experiments on shape decomposition and restoration. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(13): 85–95, 2002; Published online in Wiley Interscience (www.interscience.wiley.com). DOI 10.1002/scj.1175
On a learning theory in which pattern structure is taken into account
Authors: Uesaka Yoshinori 
Published: October 2002

AbstractIn this paper, pattern recognition is reconsidered in geometrical terms, and issues in learning theory that require further research are discussed. First, it is shown that there is learning that is easy for humans and learning that is difficult for humans, which has not been duly taken into account in existing learning theories. Then the importance of pattern structure in learning is demonstrated. For the purpose of development of a new learning theory, the structure of pattern recognition is revised, and all problems of recognition are shown to have a geometrical structure, thus being treatable by means of transformation groups. In closing, issues are put forward that should be studied in the framework of new learning theory with regard to pattern structure, and coordination between theory and experiments in pattern recognition is discussed. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(13): 103–110, 2002; Published online in Wiley InterScience (www.interscience. wiley.com). DOI 10.1002/scj.1177
Cooperative distributed registration for robust face recognition
Authors: Kato Takekazu , Mukaigawa Yasuhiro , Shakunaga Takeshi 
Published: October 2002

AbstractThis paper describes a cooperative distributed registration system for efficient acquisition of a set of facial images required in realization of robust face recognition. In this system, a lot of agents consisting of a camera and a processor are arranged, and the person detection and tracking as well as registration of facial images are integratively realized. By configuring the cooperative mechanism of this system into a three‐layer structure, the required communication capacity is reduced and efficient cooperative operation is realized. In the first layer, each agent independently performs the detection and two‐dimensional tracking of the target person. In the second layer, the robust three‐dimensional tracking is realized by cooperating agents themselves who are tracking a particular target person within an agency. In the third layer, by the cooperation among agencies, the agency configuration is dynamically changed in accordance with the position and registration conditions of the target person, and the effective registration is realized by changing over the target person of each camera. We will present the experimental results based on a system constructed with eight cameras and confirm the effectiveness of the proposed technique. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 91–100, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.1179
An e‐mail environment with handwriting using the HandsDraw digital ink format
Authors: Kato Naoki , Tanaka Hiroshi , Nakagawa Masaki 
Published: October 2002

AbstractThis paper proposes a handwriting‐based e‐mail environment system, including the HandsDraw format, whose facilities include the reading and writing of handwritten massages, their transmission and reception, annotations or comments by recipients, confirmation of the author and time of writing, and reproduction of handwriting. The system has a user interface which is friendly even to a beginner, and can handle more expressive massages on the Internet. The system is regarded as an advanced mobile communication terminal of the kind which has been fashionable recently. Considering the advantages and disadvantages of pen input, encircling (lasso) selection and a button interface are used for dialogue. Users' opinions (collected by questionnaires, on the Internet, and from laboratory use of the system for 2 1/2 years) confirm all of the functions of the system. Some respondents have suggested the conversion of handwritten characters to a type font (rather than sending them directly) by using the character‐recognition facility in this system. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 101–109, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.1180