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91.
92.
Ricchiuto P Rocco AG Gianazza E Corrada D Beringhelli T Eberini I 《Journal of molecular recognition : JMR》2008,21(5):348-354
Chicken liver bile acid binding protein (cL-BABP) crystallizes with water molecules in its binding site. To obtain insights on the role of internal water, we performed two 100 ns molecular dynamics (MD) simulations in explicit solvent for cL-BABP, as apo form and as a complex with two molecules of cholic acid, and analyzed in detail the dynamics properties of all water molecules. The diffusion coefficients of the more persistent internal water molecules are significantly different from the bulk, but similar between the two protein forms. A different number of molecules and a different organization are observed for apo- and holo-cL-BABP. Most water molecules identified in the binding site of the apo-crystal diffuse to the bulk during the simulation. In contrast, almost all the internal waters of the holo-crystal maintain the same interactions with internal sidechains and ligands, which suggests they have a relevant role in protein-ligand molecular recognition. Only in the presence of these water molecules we were able to reproduce, by a classical molecular docking approach, the structure of the complex cL-BABP::cholic acid with a low ligand root mean square deviation (RMSD) with respect to its reference positioning. Literature data reported a conserved pattern of hydrogen bonds between a single water molecule and three amino acid residues of the binding site in a series of crystallized FABP. In cL-BABP, the interactions between this conserved water molecule and the three residues are present in the crystal of both apo- and holo-cL-BABP but are lost immediately after the start of molecular dynamics. Copyright (c) 2008 John Wiley & Sons, Ltd. 相似文献
93.
94.
Stephen L. Lapointe Wayne B. Hunter Rocco T. Alessandro 《Agricultural and Forest Entomology》2004,6(4):251-257
Abstract 1 External gland openings and associated structures on the elytra of teneral and mature Diaprepes root weevils, Diaprepes abbreviatus (L.), were elucidated by scanning electron microscopy (SEM). 2 There were clear differences between teneral, callow adults and fully mature adults. In the field, teneral adults remain in the pupal chamber in the soil until sclerotization of the cuticle is complete or nearly so. 3 Phenotypic variation of the elytra in this species consists of varying patterns and coloration of scaled intervals between a variable number of raised ridges devoid of scales. In addition to being thinner and lighter in colour than fully mature adults, the elytra of teneral adults were devoid of waxy hydrocarbon secretions. 4 External gland openings at the base of each scale were observed on teneral elytra and mature elytra washed with methylene chloride. 5 SEM evidence to document the production of waxy filaments by these glands and partial characterization of these by gas chromatography and mass spectrometry are presented. 相似文献
95.
96.
Leonard H. Epstein Constance C. Gordy Hollie A. Raynor Marlene Beddome Colleen K. Kilanowski Rocco Paluch 《Obesity (Silver Spring, Md.)》2001,9(3):171-178
Objective: The goal of this study was to evaluate the effect of a parent‐focused behavioral intervention on parent and child eating changes and on percentage of overweight changes in families that contain at least one obese parent and a non‐obese child. Research Methods and Procedures: Families with obese parents and non‐obese children were randomized to groups in which parents were provided a comprehensive behavioral weight‐control program and were encouraged to increase fruit and vegetable intake or decrease intake of high‐fat/high‐sugar foods. Child materials targeted the same dietary changes as their parents without caloric restriction. Results: Changes over 1 year showed that treatment influenced targeted parent and child fruit and vegetable intake and high‐fat/high‐sugar intake, with the Increase Fruit and Vegetable group also decreasing their consumption of high‐fat/high‐sugar foods. Parents in the increased fruit and vegetable group showed significantly greater decreases in percentage of overweight than parents in the decreased high‐fat/high‐sugar group. Discussion: These results suggest that focusing on increasing intake of healthy foods may be a useful approach for nutritional change in obese parents and their children. 相似文献
97.
In prokaryotes, the RecA protein plays a pivotal role in homologous recombination, catalyzing the transfer of a single DNA
strand into an homologous molecule. Structural homologs of the bacterial RecA protein, called Rad51, have been found in different
eukaryotes (from yeast to man), suggesting a certain level of conservation in recombination pathways among living organisms.
We have cloned the homolog of RAD51 in Caenorhabditis elegans. The CeRAD51 gene is transcribed into two alternative mRNAs and potentially codes for two proteins of 395 and 357 amino acids in length,
respectively. We discuss the evolutionary implications of these findings.
Received: 26 May 1998 / Accepted: 18 August 1998 相似文献
98.
Emre Brookes Borries Demeler Camillo Rosano Mattia Rocco 《European biophysics journal : EBJ》2010,39(3):423-435
The interpretation of solution hydrodynamic data in terms of macromolecular structural parameters is not a straightforward
task. Over the years, several approaches have been developed to cope with this problem, the most widely used being bead modeling
in various flavors. We report here the implementation of the SOMO (SOlution MOdeller; Rai et al. in Structure 13:723–734,
2005) bead modeling suite within one of the most widely used analytical ultracentrifugation data analysis software packages, UltraScan
(Demeler in Modern analytical ultracentrifugation: techniques and methods, Royal Society of Chemistry, UK, 2005). The US-SOMO version is now under complete graphical interface control, and has been freed from several constraints present
in the original implementation. In the direct beads-per-atoms method, virtually any kind of residue as defined in the Protein
Data Bank (e.g., proteins, nucleic acids, carbohydrates, prosthetic groups, detergents, etc.) can be now represented with
beads whose number, size and position are all defined in user-editable tables. For large structures, a cubic grid method based
on the original AtoB program (Byron in Biophys J 72:408–415, 1997) can be applied either directly on the atomic structure, or on a previously generated bead model. The hydrodynamic parameters
are then computed in the rigid-body approximation. An extensive set of tests was conducted to further validate the method,
and the results are presented here. Owing to its accuracy, speed, and versatility, US-SOMO should allow to fully take advantage
of the potential of solution hydrodynamics as a complement to higher resolution techniques in biomacromolecular modeling. 相似文献
99.
100.
Irene Zubiri Vittoria Lombardi Michael Bremang Vikram Mitra Giovanni Nardo Rocco Adiutori Ching-Hua Lu Emanuela Leoni Ping Yip Ozlem Yildiz Malcolm Ward Linda Greensmith Caterina Bendotti Ian Pike Andrea Malaspina 《Molecular neurodegeneration》2018,13(1):60