bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling protein complexes with BiGGER
Authors: Krippahl Ludwig , Moura José J. , Palma P. Nuno 
Published: May 2003

AbstractThis article describes the method and results of our participation in the Critical Assessment of PRediction of Interactions (CAPRI) experiment, using the protein docking program BiGGER (Bimolecular complex Generation with Global Evaluation and Ranking) (Palma et al., Proteins 2000;39:372–384). Of five target complexes (CAPRI targets 2, 4, 5, 6, and 7), only one was successfully predicted (target 6), but BiGGER generated reasonable models for targets 4, 5, and 7, which could have been identified if additional biochemical information had been available. Proteins 2003;52:19–23. © 2003 Wiley‐Liss, Inc.
ZDOCK predictions for the CAPRI challenge
Authors: Chen Rong , Tong Weiwei , Mintseris Julian , Li Li , Weng Zhiping 
Published: May 2003

AbstractThe CAPRI Challenge is a blind test of protein–protein‐docking algorithms that predict the complex structure from the crystal structures of the interacting proteins. We participated in both rounds of this blind test and submitted predictions for all seven targets, relying mainly on our Fast Fourier Transform based algorithm ZDOCK that combines shape complementarity, desolvation, and electrostatics. Our group made good predictions for three targets and had at least some success with three others. Implications of the treatment of prior biological information as well as contributions of manual inspection to docking predictions are also discussed. Proteins 2003;52:68–73. © 2003 Wiley‐Liss, Inc.
A protein–protein docking benchmark
Authors: Chen Rong , Mintseris Julian , Janin Joël , Weng Zhiping 
Published: May 2003

AbstractWe have developed a nonredundant benchmark for testing protein–protein docking algorithms. Currently it contains 59 test cases: 22 enzyme‐inhibitor complexes, 19 antibody‐antigen complexes, 11 other complexes, and 7 difficult test cases. Thirty‐one of the test cases, for which the unbound structures of both the receptor and ligand are available, are classified as follows: 16 enzyme‐inhibitor, 5 antibody‐antigen, 5 others, and 5 difficult. Such a centralized resource should benefit the docking community not only as a large curated test set but also as a common ground for comparing different algorithms. The benchmark is available at (http://zlab.bu.edu/∼rong/dock/benchmark.shtml). Proteins 2003;52:88–91. © 2003 Wiley‐Liss, Inc.
Weighted geometric docking: Incorporating external information in the rotation‐translation scan
Authors: Ben‐Zeev Efrat , Eisenstein Miriam 
Published: May 2003

AbstractWeighted geometric docking is a prediction algorithm that matches weighted molecular surfaces. Each molecule is represented by a grid of complex numbers, storing information about the shape of the molecule in the real part and weight information in the imaginary part. The weights are based on experimental biochemical and biophysical data or on theoretical analyses of amino acid conservation or correlation patterns in multiple‐sequence alignments of homologous proteins. Only a few surface residues on either one or both molecules are weighted. In contrast to methods that use postscan filtering based on biochemical information, our method incorporates the external data in the rotation‐translation search, producing a different set of docking solutions biased toward solutions in which the up‐weighted residues are at the interface. Similarly, interactions involving specified residues can be impeded. The weighted geometric algorithm was applied to five systems for which regular geometric docking of the unbound molecules gave poor results. We obtained much better ranking of the nearly correct prediction and higher statistical significance when weighted geometric docking was used. The method was successful even when the weighted portion of the surface corresponded only partially and approximately to the binding site. Proteins 2003;52:24–27. © 2003 Wiley‐Liss, Inc.
Prediction of the unknown: Inspiring experience with the CAPRI experiment
Authors: Ben‐Zeev Efrat , Berchanski Alexander , Heifetz Alexander , Shapira Boaz , Eisenstein Miriam 
Published: May 2003

AbstractWe submitted predictions for all seven targets in the CAPRI experiment. For four targets, our submitted models included acceptable, medium accuracy predictions of the structures of the complexes, and for a fifth target we identified the location of the binding site of one of the molecules. We used a weighted‐geometric docking algorithm in which contacts involving specified parts of the surfaces of either one or both molecules were up‐weighted or down‐weighted. The weights were based on available structural and biochemical data or on sequence analyses. The weighted‐geometric docking proved very useful for five targets, improving the complementarity scores and the ranks of the nearly correct solutions, as well as their statistical significance. In addition, the weighted‐geometric docking promoted formation of clusters of similar solutions, which include more accurate predictions. Proteins 2003;52:41–46. © 2003 Wiley‐Liss, Inc.
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
Authors: Méndez Raúl , Leplae Raphaël , De Maria Leonardo , Wodak Shoshana J. 
Published: May 2003

AbstractThe current status of docking procedures for predicting protein–protein interactions starting from their three‐dimensional structure is assessed from a first major evaluation of blind predictions. This evaluation was performed as part of a communitywide experiment on Critical Assessment of PRedicted Interactions (CAPRI). Seven newly determined structures of protein–protein complexes were available as targets for this experiment. These were the complexes between a kinase and its protein substrate, between a T‐cell receptor β‐chain and a superantigen, and five antigen‐antibody complexes. For each target, the predictors were given the experimental structures of the free components, or of one free and one bound component in a random orientation. The structure of the complex was revealed only at the time of the evaluation. A total of 465 predictions submitted by 19 groups were evaluated. These groups used a wide range of algorithms and scoring functions, some of which were completely novel. The quality of the predicted interactions was evaluated by comparing residue–residue contacts and interface residues to those in the X‐ray structures and by analyzing the fit of the ligand molecules (the smaller of the two proteins in the complex) or of interface residues only, in the predicted versus target complexes. A total of 14 groups produced predictions, ranking from acceptable to highly accurate for five of the seven targets. The use of available biochemical and biological information, and in one instance structural information, played a key role in achieving this result. It was essential for identifying the native binding modes for the five correctly predicted targets, including the kinase‐substrate complex where the enzyme changes conformation on association. But it was also the cause for missing the correct solution for the two remaining unpredicted targets, which involve unexpected antigen‐antibody binding modes. Overall, this analysis reveals genuine progress in docking procedures but also illustrates the remaining serious limitations and points out the need for better scoring functions and more effective ways for handling conformational flexibility. Proteins 2003;52:51–67. © 2003 Wiley‐Liss, Inc.
Successful discrimination of protein interactions
Authors: Camacho Carlos J. , Gatchell David W. 
Published: May 2003

AbstractWe present results from the prediction of protein complexes associated with the first Critical Assessment of PRediction of Interactions (CAPRI) experiment. Our algorithm, SmoothDock, comprises four steps: (1) we perform rigid body docking using the program DOT, keeping the top 20,000 structures as ranked by surface complementarity; (2) we rerank these structures according to a free energy estimate that includes both desolvation and electrostatics and retain the top 2000 complexes; (3) we cluster the filtered complexes using a pairwise root‐mean‐square deviation (RMSD) criterion; (4) the 25 largest clusters are subject to a smooth docking discrimination algorithm where van der Waals forces are taken into account. We predicted targets 1, 6, and 7 with RMSDs of 9.5, 2.4, and 2.6 Å, respectively. More importantly, from the perspective of biological applications, our approach consistently ranked the correct model first (i.e., with highest confidence). For target 5 we identified the binding region but not the correct orientation. Although we were able to find reasonable clusters for all targets, low‐affinity complexes (Kd < nM) were harder to discriminate. For four of seven targets, the top models predicted by our automated procedure were among the best communitywide predictions. Proteins 2003;52:92–97. © 2003 Wiley‐Liss, Inc.
Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information
Authors: Law Dennis S. , Ten Eyck Lynn F. , Katzenelson Omer , Tsigelny Igor , Roberts Victoria A. , Pique Mike E. , Mitchell Julie C. 
Published: May 2003

AbstractWe present an evaluation of our results for the first Critical Assessment of PRedicted Interaction (CAPRI). The methods used include the molecular docking program DOT, shape analysis tool FADE, cluster analysis and filtering based on biological data. Good results were obtained for most of the seven CAPRI targets, and for two systems, submissions having the highest number of correctly predicted contacts were produced. Proteins 2003;52:33–40. © 2003 Wiley‐Liss, Inc.
Evaluation of the 3D‐Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial
Authors: Smith Graham R. , Sternberg Michael J.E. 
Published: May 2003

AbstractThe 3D‐Dock suite of programs has been used to make predictions for the seven targets in rounds 1 and 2 of the CAPRI method evaluation exercise. Some correct contacts were obtained in at least one prediction for four of seven targets. Target 06 was predicted very well, with an RMSD of the ligand after superimposition of the receptor of only 0.77 Å. We investigate the performance of the various stages of the method, with the aim of finding where improvements need to be made, and in particular whether the manual interventions that were made were essential, and whether results of the level of accuracy obtained for target 06 may be expected with confidence. Proteins 2003;52:74–79. © 2003 Wiley‐Liss, Inc.
Taking geometry to its edge: Fast unbound rigid (and hinge‐bent) docking
Authors: Schneidman‐Duhovny Dina , Inbar Yuval , Polak Vladimir , Shatsky Maxim , Halperin Inbal , Benyamini Hadar , Barzilai Adi , Dror Oranit , Haspel Nurit , Nussinov Ruth , Wolfson Haim J. 
Published: May 2003

AbstractWe present a very efficient rigid “unbound” soft docking methodology, which is based on detection of geometric shape complementarity, allowing liberal steric clash at the interface. The method is based on local shape feature matching, avoiding the exhaustive search of the 6D transformation space. Our experiments at CAPRI rounds 1 and 2 show that although the method does not perform an exhaustive search of the 6D transformation space, the “correct” solution is never lost. However, such a solution might rank low for large proteins, because there are alternatives with significantly larger geometrically compatible interfaces. In many cases this problem can be resolved by successful a priori focusing on the vicinity of potential binding sites as well as the extension of the technique to flexible (hinge‐bent) docking. This is demonstrated in the experiments performed as a lesson from our CAPRI experience. Proteins 2003;52:107–112. Published 2003 Wiley‐Liss, Inc.
Fold recognition with minimal gaps
Authors: Chen William , Mirny Leonid , Shakhnovich Eugene I. 
Published: May 2003

AbstractHere we present a simplified form of threading that uses only a 20 × 20 two‐body residue‐based potential and restricted number of gaps. Despite its simplicity and transparency the Monte Carlo‐based threading algorithm performs very well in a rigorous test of fold recognition. The results suggest that by simplifying and constraining the decoy space, one can achieve better fold recognition. Fold recognition results are compared with and supplemented by a PSI‐BLAST search. The statistical significance of threading results is rigorously evaluated from statistics of extremes by comparison with optimal alignments of a large set of randomly shuffled sequences. The statistical theory, based on the Random Energy Model, yields a cumulative statistical parameter, ϵ, that attests to the likelihood of correct fold recognition. A large ϵ indicates a significant energy gap between the optimal alignment and decoy alignments and, consequently, a high probability that the fold is correctly recognized. For a particular number of gaps, the ϵ parameter reaches its maximal value, and the fold is recognized. As the number of gaps further increases, the likelihood of correct fold recognition drops off. This is because the decoy space is small when gaps are restricted to a small number, but the native alignment is still well approximated, whereas unrestricted increase of the number of gaps leads to rapid growth of the number of decoys and their statistical dominance over the correct alignment. It is shown that best results are obtained when a combination of one‐, two‐, and three‐gap threading is used. To this end, use of the ϵ parameter is crucial for rigorous comparison of results across the different decoy spaces belonging to a different number of gaps. Proteins 2003;51:531–543. © 2003 Wiley‐Liss, Inc.
The effects of die shapes and additives on the physical and biodegradable properties of biodegradable cushioning extruded foams
Authors: Lui Wai‐Bun , Peng Jinchyau 
Published: June 2003

AbstractIn this study, efforts were focused on the effects of the operating parameters, i.e. die shapes (DS), PVA ratio (PR), additives (AT) on the physical and biodegradable properties of the corn/PVA extrudates. We also evaluated the extrudates as cushioning materials. The process variables were the operating, conditions, die shapes (○, ∞, ▵ and O), PVA ratio (40%, 50%, 60%) and additives [sodium bicarbonate (NaHCO3), calcium carbonate (CaCO3) and calcium hydroxide (Ca(OH)2)]. The experiment is a 4 × 3 × 3 factorial design. Samples of each treatment were collected and the physical, mechanical and chemical properties were measured and analysed using the PROC ANOVA and PROC CORR of the SAS 6.0 software package.35 The experimental results indicated that: (a) The change of die shapes (DS) had a significant effect on the longitudinal expansion, bulk density, compressibility and biodegradability properties of the extrudates; (b) the change of PVA ratio (PR) had a significant effect on the longitudinal expansion, bulk density and compressibility, but no effect on the biodegradability properties of the extrudates; and (c) the change of additives (AT) had a significant effect on the longitudinal expansion, bulk density and compressibility, but no effect on the spring index of the extrudates. Copyright © 2003 John Wiley & Sons, Ltd.
Packaging scorecard – a packaging performance evaluation method
Authors: Olsmats Carl , Dominic Chris 
Published: June 2003

AbstractTo support a more holistic approach to the contribution of packaging to efficiency and value creation in the product supply chain, a systematic evaluation method – packaging scorecard – has been developed and tested in two case studies. The packaging scorecard is based on research of functional criteria of packaging and the theories of ‘balanced scorecard’, a general management approach to evaluating organizational performance using different perspectives. The results of the case studies indicate that the method can be very useful to get a systematic overview of packaging performance throughout the product supply chain. Copyright © 2003 John Wiley & Sons, Ltd.
Evaluation of a UV absorber added to PET bottles for edible oil packaging
Authors: Coltro Leda , Padula Marisa , Saron Elisabete Segantini , Borghetti Joyce , Buratin Ana Elisa Penteado 
Published: June 2003

AbstractThe photo‐oxidation of lipids has significant effects on the quality of edible oils. The oxidation of oils and fats can begin due to the action of external energy sources such as light. Studies showed that the rate of photo‐oxidation of the oil depends on the light transmission of the packaging, the product characteristics and the O2 barrier of the packaging. The UV absorber 2‐(2′‐hydroxy‐3′‐tert‐butyl‐5′‐methylphenyl)‐5‐chlorobenzotriazole (Tinuvin 326™) has been used in PET bottles for oil, making possible the reduction of the photo‐oxidation rates. This additive was approved recently by the European Union and included in the Positive List of Directive 2001/62/EC, with a limit of specific migration. This additive is also approved by the Mercosur legislation; nevertheless its restriction of use is being reviewed in Brazil. This study had the objectives of evaluating the efficiency of the additive through the determination of the light barrier properties of PET bottles with various levels of Tinuvin 326™ and of verifying its suitability for use in direct contact with foods. Copyright © 2003 John Wiley & Sons, Ltd.
Fuzzy logic controller in a packaging plant
Authors: Braglia Marcello , Frosolini Marco , Montanari Roberto 
Published: June 2003

AbstractThis paper deals with the analysis of a controller used to synchronize two parallel belt conveyors in a packaging plant. A first conveyor carries the products, while the second delivers the packages. The insertion is obtained by a proper mechanical action. The control system is based on a ‘hybrid’ fuzzy logic controller, whose parameters are optimized by using an advanced ‘operational’ genetic algorithm. ‘Hybrid’ means that a conventional fuzzy logic controller is integrated with a set of special rules needed to solve particular situations characterizing the system. An important constraint is given, since the physical structure of the existing control system is to be kept unchanged. It is shown that the controller efficiently governs the belt conveyors when: (a) the distances between goods and the relative packages become higher than a certain value; (b) the performance of the electrical engine deteriorates during working time; and also (c) interference phenomena occur between consecutive good‐package couples. Copyright ©2003 John Wiley & Sons, Ltd.
Output regulation of discrete‐time linear plants subject to state and input constraints
Authors: Shi Guoyong , Saberi Ali , Stoorvogel Anton A. , Sannuti Peddapullaiah 
Published: May 2003

AbstractDiscrete‐time output regulation of linear systems with state and/or input constraints on magnitude is considered. Structural properties of linear plants are identified under which the so‐called constrained semi‐global and global output regulation problems are solvable. As in the case of continuous‐time systems, an important aspect of our development is a taxonomy of constraints showing a clear relationship between the constraint types and the output regulation results. Solvability conditions are developed for semi‐global and global output regulation problems. Appropriate regulators are constructed for problems that are solvable. Copyright © 2003 John Wiley & Sons, Ltd.
Robustness analysis of flexible structures: practical algorithms
Authors: Ferreres Gilles , Magni Jean‐François , Biannic Jean‐Marc 
Published: May 2003

AbstractWhen analysing the robustness properties of a flexible system, the classical solution, which consists of computing lower and upper bounds of the structured singular value (s.s.v.) at each point of a frequency gridding, appears unreliable. This paper describes two algorithms, based on the same technical result: the first one directly computes an upper bound of the maximal s.s.v. over a frequency interval, while the second one eliminates frequency intervals, inside which the s.s.v. is guaranteed to be below a given value. Various strategies are then proposed, which combine these two techniques, and also integrate methods for computing a lower bound of the s.s.v. The computational efficiency of the scheme is illustrated on a real‐world application, namely a telescope mock‐up which is significant of a high order flexible system. Copyright © 2003 John Wiley & Sons, Ltd.
On theLp(ℓp) stabilization of open‐loop neutrally stable linear plants with input subject to amplitude saturation
Authors: Shi Guoyong , Saberi Ali , Stoorvogel Anton A. 
Published: May 2003

AbstractIt has been shown that for asymptotically null controllable linear systems with input saturation and non‐input‐additive disturbances, there existnonlinearcontrol laws that achieve global stabilization andLp(ℓp) stabilization without finite‐gain for any p∈[1,∞). Recently, it also has been shown that for a simple double integrator there is no saturated linear controller that can achieveLpstabilization forp>2. In this paper, we show that if a linear system is open‐loop neutrally stable and stabilizable then there exist saturatedlinearcontrol laws that achieveLp(ℓp) stability for anyp∈[1,∞) and for arbitrary initial conditions. As a byproduct, we also show that the closed‐loop system with a saturated linear control law has a nice property similar to linear systems, i.e., any vanishing disturbance produces a vanishing state with arbitrary initial condition. Copyright © 2003 John Wiley & Sons, Ltd.
Robust stability, stabilization and ℋ∞ control of time‐delay systems with Markovian jump parameters
Authors: Mahmoud Magdi S. , Shi Peng 
Published: May 2003

AbstractIn this paper, the problems of stochastic stability and stabilization for a class of uncertain time‐delay systems with Markovian jump parameters are investigated. The jumping parameters are modelled as a continuous‐time, discrete‐state Markov process. The parametric uncertainties are assumed to be real, time‐varying and norm‐bounded that appear in the state, input and delayed‐state matrices. The time‐delay factor is constant and unknown with a known bound. Complete results for both delay‐independent and delay‐dependent stochastic stability criteria for the nominal and uncertain time‐delay jumping systems are developed. The control objective is to design a state feedback controller such that stochastic stability and a prescribed ℋ∞‐performance are guaranteed. We establish that the control problem for the time‐delay Markovian jump systems with and without uncertain parameters can be essentially solved in terms of the solutions of a finite set of coupled algebraic Riccati inequalities or linear matrix inequalities. Extension of the developed results to the case of uncertain jumping rates is also provided. Copyright © 2003 John Wiley & Sons, Ltd.
Physicochemical Properties of Sweet Potato Flour and Starch as Affected by Blanching and Processing
Authors: Jangchud Kamolwan , Phimolsiripol Yuthana , Haruthaithanasan Vichai 
Published: June 2003

AbstractThe effects of blanching on physicochemical properties of flours and starches prepared from two varieties of sweet potatoes (Mun‐Kai and Negro) were studied and compared. The pasting temperature and peak viscosity of starches, respectively, were 74 and 80 °C and 381 and 433 RVU. The pasting temperature (74.0‐94.8 °C) of flours was greater than that of starch, depending on the variety and blanching process. However, the peak viscosity (ca. 103‐120 RVU) of flours was lower than that of the corresponding starches. Partial gelatinization of starch granules was observed as a result of a 1‐min blanching. Composition of starch and flour was found to affect swelling power and solubility. The starch content of starches, flours from unblanched sweet potato and flours from 1‐min blanched sweet potatoes were 97; 66.3 and 74.9; as well as 36.6 and 40.4%, respectively. Amylose content of flours and starches varied from 17.2‐20.8%.