bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building alternate protein structures using the elastic network model
Authors: Yang Qingyi , Sharp Kim A. 
Published: August 2008

AbstractWe describe a method for efficiently generating ensembles of alternate, all‐atom protein structures that (a) differ significantly from the starting structure, (b) have good stereochemistry (bonded geometry), and (c) have good steric properties (absence of atomic overlap). The method uses reconstruction from a series of backbone framework structures that are obtained from a modified elastic network model (ENM) by perturbation along low‐frequency normal modes. To ensure good quality backbone frameworks, the single force parameter ENM is modified by introducing two more force parameters to characterize the interaction between the consecutive carbon alphas and those within the same secondary structure domain. The relative stiffness of the three parameters is parameterized to reproduce B‐factors, while maintaining good bonded geometry. After parameterization, violations of experimental CαCα distances and CαCαCα pseudo angles along the backbone are reduced to less than 1%. Simultaneously, the average B‐factor correlation coefficient improves to R = 0.77. Two applications illustrate the potential of the approach. (1) 102,051 protein backbones spanning a conformational space of 15 Å root mean square deviation were generated from 148 nonredundant proteins in the PDB database, and all‐atom models with minimal bonded and nonbonded violations were produced from this ensemble of backbone structures using the SCWRL side chain building program. (2) Improved backbone templates for homology modeling. Fifteen query sequences were each modeled on two targets. For each of the 30 target frameworks, dozens of improved templates could be produced In all cases, improved full atom homology models resulted, of which 50% could be identified blind using the D‐Fire statistical potential. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions
Authors: Koch Oliver , Klebe Gerhard 
Published: August 2008

AbstractTurns are irregular secondary structure elements with a hydrogen bond or a specific Cα‐Cα distance between the first and the last residue. They are up to six residues in length. Here, we present a uniform classification for all normal (COi – NHi+n hydrogen bond), open (a Cαi‐Cαi+n distance up to 10 Å), and reverse (NHi – COi+i hydrogen bond) turn families based on current structural data. Considering the large amount of data evaluated, this classification likely covers quite comprehensively most of the possible conformations of turns. All turn structures of a nonredundant dataset of 1903 protein chains were retrieved using Relibase and clustered using emergent self‐organizing maps. This leads to three normal, four open, and five reverse turn families with several new turn‐types. Based on the amino acid propensities, the achieved separation into normal, open, and reverse turn families seems convincing. In combination with β‐sheet and helix classification on average 96% of the given protein chain can now be successfully classified. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Docking and scoring with alternative side‐chain conformations
Authors: Hartmann Christoph , Antes Iris , Lengauer Thomas 
Published: August 2008

AbstractWe describe a scoring and modeling procedure for docking ligands into protein models that have either modeled or flexible side‐chain conformations. Our methodical contribution comprises a procedure for generating new potentials of mean force for the ROTA scoring function which we have introduced previously for optimizing side‐chain conformations with the tool IRECS. The ROTA potentials are specially trained to tolerate small‐scale positional errors of atoms that are characteristic of (i) side‐chain conformations that are modeled using a sparse rotamer library and (ii) ligand conformations that are generated using a docking program. We generated both rigid and flexible protein models with our side‐chain prediction tool IRECS and docked ligands to proteins using the scoring function ROTA and the docking programs FlexX (for rigid side chains) and FlexE (for flexible side chains). We validated our approach on the forty screening targets of the DUD database. The validation shows that the ROTA potentials are especially well suited for estimating the binding affinity of ligands to proteins. The results also show that our procedure can compensate for the performance decrease in screening that occurs when using protein models with side chains modeled with a rotamer library instead of using X‐ray structures. The average runtime per ligand of our method is 168 seconds on an Opteron V20z, which is fast enough to allow virtual screening of compound libraries for drug candidates. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Fragment‐based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities
Authors: Li Quan , Zhou Changhai , Liu Haiyan 
Published: August 2008

AbstractGeneral and transferable statistical potentials to quantify the compatibility between local structures and local sequences of peptide fragments in proteins were derived. In the derivation, structure clusters of fragments are obtained by clustering five‐residue fragments in native proteins based on their conformations represented by a local structure alphabet (de Brevern et al., Proteins 2000;41:271–287), secondary structure states, and solvent accessibilities. On the basis of the native sequences of the structurally clustered fragments, the probabilities of different amino acid sequences were estimated for each structure cluster. From the sequence probabilities, statistical energies as a function of sequence for a given structure were directly derived. The same sequence probabilities were employed in a database‐matching approach to derive statistical energies as a function of local structure for a given sequence. Compared with prior models of local statistical potentials, we provided an integrated approach in which local conformations and local environments are treated jointly, structures are treated in units of fragments instead of individual residues so that coupling between the conformations of adjacent residues is included, and strong interdependences between the conformations of overlapping or neighboring fragment units are also considered. In tests including fragment threading, pseudosequence design, and local structure predictions, the potentials performed at least comparably and, in most cases, better than a number of existing models applicable to the same contexts indicating the advantages of such an integrated approach for deriving local potentials and suggesting applicability of the statistical potentials derived here in sequence designs and structure predictions. Proteins 2009. © 2008 Wiley‐Liss, Inc.
MINOES: A new approach to select a representative ensemble of structures in NMR studies of (partially) unfolded states. Application to Δ25‐PYP
Authors: Krzeminski Mickaël , Fuentes Gloria , Boelens Rolf , Bonvin Alexandre M.J.J. 
Published: August 2008

AbstractIn nature, some proteins partially unfold under specific environmental conditions. These unfolded states typically consist of a large ensemble of conformations; their proper description is therefore a challenging problem. NMR spectroscopy is particularly well suited for this task: information on conformational preferences can be derived, for example, from chemical shifts or residual dipolar couplings. This information, which is measured as a time‐ and ensemble‐average, can be used to model these states by generating large ensembles of conformations. The challenge is then to select a minimum representative set of conformations out of a large ensemble to represent the unfolded state. We have developed for this purpose an algorithm called MINOES (MINimum Optimal Ensemble Selection), which is based on an iterative procedure based on a driven expansion/contraction selection process. MINOES aims at selecting an optimal and minimal ensemble of conformations that, on average, maximizes the agreement between back‐calculated and experimental (NMR) data, without any a‐priori assumption about the required ensemble size. This approach is demonstrated by modeling the partially unfolded state of a deletion mutant of the Photoactive Yellow Protein, Δ25‐PYP, which has been previously characterized by NMR (Bernard et al., Structure 2005;13:953–962). Proteins 2009. © 2008 Wiley‐Liss, Inc.
Ab initio analysis of monomers and dimers of trialkylphosphine oxides: Structural and thermodynamic stability
Authors: Malaspina Thaciana , Costa Luciano T. , Fileti Eudes E. 
Published: August 2008

AbstractStructural and thermodynamic stabilities of monomers and dimers of trialkylphosphine oxides (TRPO) were studied using quantum chemistry calculations. Density functional theory calculations were carried out and the structures of four TRPO have been determined: TMPO (methyl; R = CH3), TEPO (ethyl; R = CH3CH2), TBPO (n‐butyl; R = CH3(CH2)3), and TOPO (n‐octyl; R = CH3(CH2)7). TRPO homodimers were investigated considering two isomeric possibilities for each dimer. Relative binding energies and the enthalpic and entropic contributions to the Gibbs free energy were calculated for all dimers. The formation of dimers from the individual monomeric TRPO species as a function of temperature was also analyzed. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Computational studies on the spectroscopic properties of the 2‐pyridylpyrazolate‐based platinum(II) complexes with modified pyrazolate fragment
Authors: Bai Fu‐Quan , Zhou Xin , Liu Tao , Zhao Guang‐Jin , Zhang Jian‐Po , Zhang Hong‐Xing 
Published: August 2008

AbstractElectronic structures and spectroscopic properties of a series of platinum(II) complexes based on the 2‐pyridylpyrazolate ligand with modified pyrazolate fragment have been studied by the time‐dependent density functional theory (TD‐DFT) calculations. The ground‐ and excited‐state structures were optimized by the DFT and single‐excitation configuration interaction (CIS) methods, respectively. The calculated structures and spectroscopic properties are in agreement with the corresponding experimental results. The results of the spectroscopic investigations revealed that the lowest‐energy absorptions have 1,3MLCT/1,3ILCT mixing characters. When the electron‐withdrawing groups (CF3, C3F7) are introduced into the pyrazolate fragment, the lowest‐energy absorptions are blue‐shifted compared with that without substituents on the pyrazolate fragment, while the opposite case is observed for the electron‐donating groups (Me, tBu, etc.). Otherwise, the phosphorescent emissions of these complexes have the 3MLCT/3ILCT character and should be originated from the lowest‐energy absorptions. When the pyrazolate fragment is replaced by the indazole group, the HOMO and LUMO orbitals of the pyridyl‐indazolate ligand platinum(II) complexes have obvious π and π* orbital characters. Therefore, there is no evident MLCT character in the lowest energy absorption and emission. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Theoretical study on structures and stabilities of N4X (X = O, S, Se, Te) series
Authors: Guohua Zhang , Yongfang Zhao , Fengyou Hao , Pingxia Zhang , Xiudan Song 
Published: August 2008

AbstractThe stable and transition structures of N4X (X = O, S, Se, Te) series with singlet state are optimized with the ab initio (MP2) and density functional theory (B3LYP) methods using the 6‐311+G(d) basis set. The ring isomers are found to be the global minima for N4O, N4S, N4Se, and the chain isomer is the minimum for N4Te. The stabilities are studied by evaluating the dissociation barriers with respect to dissociation. The reactants and products connected by transition structures are determined by applying the intrinsic reaction coordinate (IRC) calculations. The C2v, C3v and ring isomers decompose into linear NNX and N2 molecules, however, the chain isomers decompose into cyclic N2X and N2 firstly. A new possible isomerization mechanism between the cyclic and linear structures of N2X series is studied. The cyclic structures of N2X convert into linear structures easily with the very low barriers. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Hepatitis C and renal transplantation: a review on historical aspects and current issues
Authors: Moghaddam Seyed Mohammadmehdi Hosseini , Alavian Seyed Moayed , Kermani Nahid Arjmand 
Published: August 2008

AbstractChronic liver disease has a significant impact on the survival of renal transplant recipients with an incidence rate of 4–38%. Approximately, 8–28% of renal transplant recipients die due to chronic liver disease. Hepatitis C seems to be the leading cause of chronic liver disease in kidney recipients. Hepatitis C virus (HCV) infection has a wide range of prevalence (2.6–66%) among renal transplant recipients living in different countries with great genotype diversity in different parts of the world. Nowadays, antiviral drugs are used for the management of hepatitis C. Because of graft‐threatening effects of some antiviral drugs used in HCV‐infected renal transplant recipients, we specifically focused on HCV treatment after renal transplantation. Treatment of post‐renal transplantation chronic liver disease with INF and ribavirin remains controversial. Anecdotal reports on post‐renal transplantation hepatitis C demonstrate encouraging findings. This review summarises the most current information on diagnosis, treatment, prognosis, complications as well as the new aspects of treatment in HCV‐infected renal transplant recipients. HCV belongs to the family of Flaviviridae, genus Hepacivirus. Copyright © 2008 John Wiley & Sons, Ltd.
The influence of human, livestock, and ecological features on the occurrence of genet (Genetta genetta): a case study on Mediterranean farmland
Authors: Galantinho Ana , Mira António 
Published: August 2008

AbstractWe have studied the relationship between occurrence patterns of the genet (Genetta genetta) and ecological, human, and livestock descriptors at the Monfurado Natura 2000 Site in southern Portugal. An information–theoretical model comparison (ITMC) was used to select the best models to explain the presence of the species, using data from 36 habitat patches. Variables that were included in the best models then were used in a variation partitioning procedure to determine the relative influence of each variable set on the presence of the genet. When considered together, all the variables captured 56.5% of the variance in genet occurrence within the study area. The set of ecological variables accounted for most of the explained variance (pure effect: 30.3%). In the best ecological model, the occurrence of the genet was positively related to the density of trees and shrubs in the dominant agro–silvo–pastoral system (montado), to soil organic matter, and to Shannon's index of vertical vegetation diversity. Human influence factors (pure effect: 4.8%) highlighted the negative relationship between the presence of the genet and the proportion of game‐estate areas. The group of livestock variables (pure effect: 8.5%) revealed that intermediate levels of grazing may promote the occurrence of the genet. Our results highlight the importance of variables directly related to agricultural management, and are meaningful because they allow for the prioritization of management decisions. In particular, the results draw attention to soil organic matter and grazing by sheep, which are important factors in soil conservation practices.
Age-related slowing of movement as basal ganglia dysfunction
Authors: Saling L. L. , Phillips J. G. 
Published: August 2008

AbstractAttributions of age-related deficits in motor function to structural changes are compromised once the elderly exhibit lower error rates. This is because performance decrements observed in older adults are attributed to inferred strategic preferences for accuracy over speed. To understand genuine age differences in performance, we argue in the following theoretical paper that research needs to resolve methodological shortcomings and account for them within theoretical models of aging. Accounts of aging need to directly manipulate or control strategic differences in performance while assessing structural deficits. When this is done, age-related changes in motor control resemble the intermittencies of control seen in basal ganglia disorders. Given homologous circuitry in the basal ganglia, such observations could generalize to age-related changes in cognitive and emotional processes.
Batteries assessing health related fitness in the elderly: a brief review
Authors: Varela S. , Ayán C. , Cancela J. M. 
Published: August 2008

Abstract
Evaluation of physical functioning is a key issue in clinical geriatrics and in aging research. In recent years, different physical performance batteries in which individuals are asked to perform several tasks and are evaluated using different criteria have been designed and used in elderly populations. These batteries include different types of test which range from basic motor abilities to relevant everyday activities, depending on the construct area in the domain of physical function that must be measured. This paper reviews and classifies the main physical functioning batteries that can be found in the scientific field of aging research in order to provide knowledge on selection, administration, and interpretation of this indispensable assessment tools.
Toward Understanding Molecular Mechanisms of Abiotic Stress Responses in Rice
Authors: Gao Ji-Ping , Chao Dai-Yin , Lin Hong-Xuan 
Published: August 2008

AbstractPlants have evolved delicate mechanisms to cope with environmental stress. Following exposure to environmental stimuli, extracellular signals are perceived and transmitted through signal transduction cascades. Upon receipt and transmission of the signals, a number of stress-related genes are induced, leading to stress adaptation in plant cells. Rice, which is a critical food grain for a large portion of the world’s population, is frequently impacted by several abiotic stressors, the most important of which are drought, salinity, and cold. Exposure to environmental conditions outside of acceptable tolerance ranges can negatively affect rice growth and production. In this paper, a review of rice responses to abiotic stress is presented, with particular attention to the genes and pathways related to environmental stress tolerance. It is apparent that, while progress has been made in identifying genes involved in stress adaptation, many questions remain. Understanding the mechanisms of stress response in rice is important for all research designed to develop new rice varieties with improved tolerance.
The Cornucopia of Small RNAs in Plant Genomes
Authors: Simon Stacey A. , Zhai Jixian , Zeng Jia , Meyers Blake C. 
Published: August 2008

AbstractRegulatory small RNAs (approximately 20 to 24 nt in length) are produced through pathways that involve several key evolutionarily conserved protein families; the variants of these proteins found in plants are encoded by multigene families and are known as Dicer-like, Argonaute, and RNA-dependent RNA polymerase proteins. Small RNAs include the well-known classes of microRNAs (miRNAs, ~21 nt) and the small-interfering RNAs (siRNAs, ~24 nt). Both of these types of molecules are found across a broad set of eukaryotic species, although the siRNAs are a much larger and more diverse class in plants due to the abundance of heterochromatic siRNAs. Well-studied species such asArabidopsishave provided a foundation for understanding in rice and other species how small RNAs function as key regulators of gene expression. In this paper, we review the current understanding of plant small RNA pathways, including the biogenesis and function of miRNAs, siRNAs, trans-acting siRNAs, and heterochromatic siRNAs. We also examine the evolutionary relationship among plant species of both their miRNAs and the key enzymatic components of the small RNA pathways. Many of the most recent advances in describing small RNAs have resulted from advances in sequencing technologies used for identifying and measuring small RNAs, and these technologies are discussed. Combined with the plethora of genetic tools available to researchers, we expect that the continued elucidation of the identity and functions of plant small RNAs will be both exciting and rewarding.
Rice Metabolomics
Authors: Oikawa Akira , Matsuda Fumio , Kusano Miyako , Okazaki Yozo , Saito Kazuki 
Published: August 2008

AbstractMetabolomics is a recently developed technology for comprehensive analysis of metabolites in organisms. Plant metabolites that are produced for the growth, development, and chemical defense of plants against climatic alterations or natural predators are also useful to us as nutrients or medicines; hence, it is important to comprehend the amounts and varieties of plant metabolites. Besides providing an understanding of the metabolic state in plants under various circumstances, metabolomic techniques are applicable to the clarification of the functions of unknown genes by using natural variants or mutants of the target plants. Furthermore, a metabolomic approach might be useful in the breeding of crops, since valuable plant traits such as taste and yield are closely related to metabolic conditions. Here, we describe the methodology of metabolomics including sample extraction and preparation, metabolite detection, and data processing and analysis, and introduce the application of metabolomic studies to rice.
Negative and positive peer influence: Relations to positive and negative behaviors for African American, European American, and Hispanic adolescents
Authors: Padilla‐Walker Laura M. , Bean Roy A. 
Published: August 2008

ABSTRACTThe purpose of the current study was to examine adolescents' perceptions of negative and positive peer influence (i.e., indirect peer association and direct peer pressure) as they related to adolescent behavior. Regression analyses were conducted using a sample of African American, European American, and Hispanic adolescents (N = 1659, M age = 16.06, SD = 1.10). The study found differences and similarities in relation to respondents' ethnicity vis‐à‐vis indirect peer association and adolescent behavior. Although few ethnic‐based differences occurred as a function of indirect negative peer association, indirect positive peer association was not as consistently or as strongly related to behaviors for minority youth as it was for European American youth.
The influence of a primary prevention program on eating‐related attitudes of Israeli female middle‐school students
Authors: Canetti Laura , Bachar Eytan , Gur Eitan , Stein Daniel 
Published: August 2008

ABSTRACTThe present study aimed to assess the impact of a primary prevention program on eating‐related attitudes in 231 female 7th graders at baseline and following a six‐session prevention program. Fifty‐nine 7th grade control females received six unstructured lectures about adolescence. One hundred and three experimental students and 37 controls were re‐evaluated after one year. Among the participants in the prevention program, there was a significant post‐intervention and one‐year improvement in the total score of the eating‐related attitudinal Treatment Efficacy Scale (TES) and in several of its domains. Whereas no change occurred in the attitudes of the controls at post‐intervention, some improvement was shown in several TES domains after one year, compared to baseline. Attitudinal changes were significantly more favorable in the prevention program participants than in the controls both at post‐intervention and at one‐year follow‐up. These findings suggest that eating‐related attitudes of female middle‐school students may improve following a primary prevention program, with some of these improvements persisting after one year.