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Allan Peter Davis Cynthia G Murphy Cynthia A Saraceni-Richards Michael C Rosenstein Thomas C Wiegers Thomas H Hampton Carolyn J Mattingly 《Bioinformation》2009,4(4):173-174
The Comparative Toxicogenomics Database is a public resource that promotes understanding about the effects of environmental chemicals on
human health. Currently, CTD describes over 184,000 molecular interactions for more than 5,100 chemicals and 16,300 genes/proteins. We
have leveraged this dataset of chemical-gene relationships to compute similarity indices following the statistical method of the Jaccard index.
These scores are used to produce lists of comparable genes (“GeneComps”) or chemicals (“ChemComps”) based on shared toxicogenomic
profiles. GeneComps and ChemComps are now provided for every curated gene and chemical in CTD. ChemComps are particularly significant
because they provide a way to group chemicals based upon their biological effects, instead of their physical or structural properties. These metrics
provide a novel way to view and classify genes and chemicals and will help advance testable hypotheses about environmental chemical-genedisease
networks.
Availability
CTD is freely available at http://ctd.mdibl.org/ 相似文献3.
This short paper summarises the information developed in the EU funded research project STAR on autecology databases, metrics,
multimetrics and community approaches. For Europe the WFD implementation gave an important stimulus for the development of
ecology based assessment techniques. Along with the development of metrics and multimetrics indices taxalists and autecological
information were strongly improved. Recommendations are given to further develop ecological assessment in European streams
and rivers. 相似文献
4.
Vinay Singh Tanwar Mandeep P. Chand Jitender Kumar Gaurav Garg Sandeep Seth Ganesan Karthikeyan Shantanu Sengupta 《Gene》2013
Vitamin B12 is an essential micronutrient synthesized by microorganisms. Mammals including humans have evolved ways for transport and absorption of this vitamin. Deficiency of vitamin B12 (either due to low intake or polymorphism in genes involved in absorption and intracellular transport of this vitamin) has been associated with various complex diseases. Genome-wide association studies have recently identified several common single nucleotide polymorphisms (SNPs) in fucosyl transferase 2 gene (FUT2) to be associated with levels of vitamin B12—the strongest association was with a non-synonymous SNP rs602662 in this gene. In the present study, we attempted to replicate the association of this SNP (rs602662) in an Indian population since a significant proportion has been reported to have low levels of vitamin B12 in this population. A total of 1146 individuals were genotyped for this SNP using a single base extension method and association with levels of vitamin B12 was assessed in these individuals. Regression analysis was performed to analyze the association considering various confounding factors like for age, sex, diet, hypertension, diabetes mellitus and coronary artery disease status. We found that the SNP rs602662 was significantly associated with the levels of vitamin B12 (p value < 0.0001). We also found that individuals adhering to a vegetarian diet with GG (homozygous major genotype) have significantly lower levels of vitamin B12 in these individuals. Thus, our study reveals that vegetarian diet along with polymorphism in the FUT2 gene may contribute significantly to the high prevalence of vitamin B12 deficiency in India. 相似文献
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A database system and computer programs for storage and retrieval of information about guanine nucleotide-binding protein (G protein) -coupled receptor mutants and associated biological effects have been developed. Mutation data on the receptors were collected from the literature and a database of mutants and effects of mutations was developed. The G protein-coupled receptor, family A, point mutation database (GRAP) provides detailed information on ligand-binding and signal transduction properties of more than 2130 receptor mutants. The amino acid sequences of receptors for which mutation experiments have been reported were aligned, and from this alignment mutation data may be retrieved. Alternatively, a search form allowing detailed specification of which mutants to retrieve may be used, for example, to search for specific amino acid substitutions, substitutions in specific protein domains or reported biological effects. Furthermore, ligand and bibliographic oriented queries may be performed. GRAP is available on the Internet (URL: http://www-grap.fagmed.uit.no/GRAP/homepage.html ) using the World-Wide Web system. © 1996 Wiley-Liss, Inc. 相似文献
7.
The ATP-binding cassette (ABC) transporters are one of the major classes of active transporters. They are widespread in archaea, bacteria, and eukaryota, indicating that they have arisen early in evolution. They are involved in many essential physiological processes, but the majority import or export a wide variety of compounds across cellular membranes. These systems share a common architecture composed of four (exporters) or five (importers) domains. To identify and reconstruct functional ABC transporters encoded by archaeal and bacterial genomes, we have developed a bioinformatic strategy. Cross-reference to the transport classification system is used to predict the type of compound transported. A high quality of annotation is achieved by manual verification of the predictions. However, in order to face the rapid increase in the number of published genomes, we also include analyses of genomes issuing directly from the automated strategy. Querying the database (http://www-abcdb.biotoul.fr) allows to easily retrieve ABC transporter repertories and related data. Additional query tools have been developed for the analysis of the ABC family from both functional and evolutionary perspectives. 相似文献
8.
Francesco Santi;Riccardo Testolin;Piero Zannini;Michele Di Musciano;Virginia Micci;Lorenzo Ricci;Riccardo Guarino;Gianluigi Bacchetta;José María Fernández-Palacios;Mauro Fois;Konstantinos Kougioumoutzis;Kadir Boğaç Kunt;Federico Lucchi;Frédéric Médail;Toni Nikolić;Rüdiger Otto;Salvatore Pasta;Maria Panitsa;Konstantinos Proios;Spyros Sfenthourakis;Stylianos M. Simaiakis;Claudio A. Tranne;Kostas A. Triantis;Alessandro Chiarucci; 《Global Ecology and Biogeography》2024,33(8):e13855
The intrinsic characteristics of islands make them a unique study system for the investigation of ecological and evolutionary dynamics. The Mediterranean Basin, an island-rich biodiversity hotspot, still lacks a comprehensive spatial database for these geographic features. This study presents the first comprehensive spatial database of all Mediterranean islands larger than 0.01 km2, aiding ecological investigations and interdisciplinary research. 相似文献
9.
Chuanyi Yao Shaokun Tang Zhimin He Xu Deng 《Journal of Molecular Catalysis .B, Enzymatic》2005,35(4-6):108-112
The kinetics of lipase-catalyzed hydrolysis of olive oil in AOT/isooctane reversed micellar media was studied. It was shown that the deactivation of lipase had a great influence on the reaction kinetics. Based on whether the enzyme deactivation and influences of both product and substrate on enzyme stability were included or not, four different kinetic models were established. The simulating results demonstrated that the kinetic model, which including product inhibition, enzyme deactivation and the improvements of lipase stability by both product and substrate, fit the experimental data best with an overall relative error of 4.68%. 相似文献
10.
Meryem Alp Alechania Misturini German Sastre Maria Gálvez-Llompart 《Journal of cellular and molecular medicine》2023,27(15):2249-2260
In the present study, the identification of potential α-amylase inhibitors is explored as a potential strategy for treating type-2 diabetes mellitus. A computationally driven approach using molecular docking was employed to search for new α-amylase inhibitors. The interactions of potential drugs with the enzyme's active site were investigated and compared with the contacts established by acarbose (a reference drug for α-amylase inhibition) in the crystallographic structure 1B2Y. For this active site characterization, both molecular docking and molecular dynamics simulations were performed, and the residues involved in the α-amylase–acarbose complex were considered to analyse the potential drug's interaction with the enzyme. Two potential α-amylase inhibitors (AN-153I105594 and AN-153I104845) have been selected following this computational strategy. Both compounds established a large number of interactions with key binding site α-amylase amino acids and obtained a comparable docking score concerning the reference drug (acarbose). Aiming to further analyse candidates' properties, their ADME (absorption, distribution, metabolism, excretion) parameters, druglikeness, organ toxicity, toxicological endpoints and median lethal dose (LD50) were estimated. Overall estimations are promising for both candidates, and in silico toxicity predictions suggest that a low toxicity should be expected. 相似文献