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101.
《印度化学会志》2021,98(10):100156
Corona virus disease 2019 (COVID-19) endemic has havoc on the world; the causative virus of the pandemic is SARS CoV-2. Pharmaceutical companies and academic institutes are in continuous efforts to identify anti-viral therapy or vaccines, but the most significant challenge faced is the highly evolving genome of SARS CoV-2, which is imparting evolutionary selective benefits to the virus. To understand the viral mutations, we have retrieved nine hundred and thirty-four samples from different states of India via the GISAID database and analyzed the frequency of all types of point mutation in all structural, non-structural proteins, and accessory factors of SARS CoV-2. Spike glycol protein, nsp3, nsp6, nsp12, N and NS3 were the most evolving proteins. High frequency point mutations were Q496P (nsp2), A380V (nsp4), A994D (nsp3), L37F (nsp6), P323L & A97V (nsp12), Q57H (ns3), D614G (S), P13L (N), R203K (N), G204R (N) and S194L (N). 相似文献
102.
Scoring functions: A view from the bench 总被引:2,自引:0,他引:2
Tame JR 《Journal of computer-aided molecular design》1999,13(2):99-108
Computational approaches to drug design are presently hindered by the complexity of the physical chemistry which underlies weak, non- covalent interactions between protein targets and small molecule ligands. Although a number of programs are now available for the design of novel potential ligands, it remains a key problem to rank these rapidly and reliably by estimated binding affinity. Such a step is necessary to select only the most promising candidates for synthesis and experimental characterisation. To calculate ligand affinity quickly and reliably is an extremely difficult problem, but it may well prove possible to estimate sufficiently accurately given an appropriate set of parameters to score individual protein–ligand interactions. Improvements in the situation will require a wider set of thermodynamically characterised systems than is currently available. 相似文献
103.
Crude extracellular invertase fromSclerotium rolfsii, when coupled to glutaraldehyde activated Indion 48-R, retained 70–80% activity of the soluble enzyme. Immobilization resulted
in a decrease in the pH and temperature optima but it increased the temperature stability. Km and Vmax also increased as a result of immobilization. Both soluble and immobilized invertase showed inhibition at high substrate
concentrations. The bound enzyme showed excellent stability to repeated use and retained approx 90% of its initial activity
after 8 cycles of use. 相似文献
104.
The effect of calcining conditions on the rehydration of dead burnt magnesium oxide using magnesium acetate as a hydrating agent 总被引:1,自引:0,他引:1
C. A. Strydom E. M. van der Merwe M. E. Aphane 《Journal of Thermal Analysis and Calorimetry》2005,80(3):659-662
Summary Magnesium oxide was produced through calcination of magnesite ore. A rehydration percentage of MgO to Mg(OH)2 of higher than 60% is obtained using calcination temperatures of 1000°C and below. At these temperatures medium reactive MgO was formed. The extend to which dead burnt MgO (obtained after calcination at 1200°C and higher) may be rehydrated is dependent on the calcination time, but even after 1 h and using magnesium acetate as a hydrating agent only 40% of the initial product has rehydrated to Mg(OH)2. After 4 and more hours of calcinations at 1200°C, a maximum of approximately 14% of the initial MgO is rehydrated back to Mg(OH)2. Thermogravimetric analysis was performed on the various compounds to determine the amounts of Mg(OH)2 that formed. 相似文献
105.
Robert P. Apaya Baldo Lucchese Sarah L. Price J.G. Vinter 《Journal of computer-aided molecular design》1995,9(1):33-43
Summary Ligands which bind to a specific protein binding site are often expected to have a similar electrostatic environment which complements that of the binding site. One method of assessing molecular electrostatic similarity is to examine the possible overlay of the maxima and minima in the electrostatic potential outside the molecules and thereby match the regions where strong electrostatic interactions, including hydrogen bonds, with the residues of the binding site may be possible. This approach is validated with accurate calculations of the electrostatic potential, derived from a distributed multipole analysis of an ab initio charge density of the molecule, so that the effects of lone pair and -electron density are correctly included. We have applied this method to the phosphodiesterase (PDE) III substrate adenosine-3,5-cyclic monophosphate (cAMP) and a range of nonspecific and specific PDE III inhibitors. Despite the structural variation between cAMP and the inhibitors, it is possible to match three or four extrema to produce relative orientations in which the inhibitors are sufficiently sterically and electrostatically similar to the natural substrate to account for their affinity for PDE III. This matching of extrema is more apparent using the accurate electrostatic models than it was when this approach was first applied, using semiempirical point charge models. These results reinforce the hypothesis of electrostatic similarity and give weight to the technique of extrema matching as a useful tool in drug design. 相似文献
106.
H. -J. Schneider U. Schneider 《Journal of inclusion phenomena and macrocyclic chemistry》1994,19(1-4):67-83
Conformations, acid-base and supramolecular properties of phenolic metacyclophanes obtained from the condensation of resorcinol with aldehydes are discussed, including the mechanisms involved in the formation of these macrocycles. The strong binding of choline-type compounds and the inhibition of acetylcholine hydrolysis with therccc stereoisomers is mechanistically evaluated; arctt isomer shows strong conformational coupling for, e.g., choline binding and simultaneous proton release. The presence of larger alkyl residues at the bottom of therccc macrocycle leads to an additional binding site for small lipophilic substrates, which is independent of the upper complexation center for positively charged substrates. Substitution at the upper rim by carboxylic groups at the 2-position of the phenyl rings yields receptors for, e.g., , -diammonium ions with alternate equatorial and axial arylunits. Positively charged substituents at the upper rim, introduced by aminoalkylation, lead to little change of complexation as a result from their orientation away from the binding center. Aminoacid substituents, for the same reason, do not lead to enantioselective complexation, but allow particularly for strong binding of transition metal ions. Preliminary studies show that resorcinarenes bearing a wide array of positive charges are potent groove binders to ds-DNA without intercalative contributions.This paper is dedicated to the commemorative issue on the 50th anniversary of calixarenes. 相似文献
107.
Two new ditopic receptors for α,ω-alkanediyldiammonium cations based on a tetraazamacrocyclic (cyclidene) nickel(II) complex bearing two crown-ether residues were synthesized. The studies of the host-guest interaction between the receptors and a series of α,ω-diammonium salts by NMR titration in acetonitrile-d3 showed that 1:1 complexes are formed with Kassoc∼103-105 M−1. Receptor 1 with benzo-15-crown-5 arms showed substantial selectivity in binding of trimethylene- and tetramethylenediammonium dications, and 1-2 orders of magnitude weaker binding of shorter (C2) or longer (C5 and C6) diammonium cations. Receptor 2 with benzo-18-crown-6 arms showed higher affinity to all studied diammonium cations, but the recognition of the length of α,ω-diammonium cations was less pronounced. 相似文献
108.
A study of the structural stability of clusters made up of a single component has been carried out within the Embedded Atom Method. Perfect icosahedral and cuboctahedral Cu, Ni, Pd, and Ag clusters with up to 5083 atoms have been compared. The icosahedron is found to be the stable structure for small clusters, and a change of structure from icosahedral to cuboctahedral is found as the cluster size increases. A contraction of the interatomic distances results when the cluster size decreases. 相似文献
109.
Summary A molecular dynamics/energy-minimisation protocol has been used to analyse the structural and energetic effects of functional group substitution on the binding of a series of C4-modified 2-deoxy-2,3-didehydro-N-acetylneuraminic acid inhibitors to influenza virus sialidase. Based on the crystal structure of sialidase, a conformational searching protocol, incorporating multiple randomisation steps in a molecular dynamics simulation was used to generate a range of minimum-energy structures. The calculations were useful for predicting the number, location, and orientation of structural water molecules within protein-ligand complexes. Relative binding energies were calculated for the series of complexes using several empirical molecular modelling approaches. Energies were computed using molecular-mechanics-derived interactions as the sum of pairwise atomic nonbonded energies, and in a more rigorous manner including solvation effects as the change in total electrostatic energy of complexation, using a continuum-electrostatics (CE) approach. The CE approach exhibited the superior correlation with observed affinities. Both methods showed definite trends in observed and calculated binding affinities; in both cases inhibitors with a positively charged C4 substituent formed the tightest binding to the enzyme, as observed experimentally.This paper is based on a presentation given at the 14th Molecular Graphics and Modelling Society Conference, held in Cairns, Australia, August 27–September 1, 1995.Presently on a visiting postdoctoral fellowship in the Department of Biomolecular Structure, Glaxo Research & Development Ltd, Greenford, Middlesex UB6 OHE, U.K. 相似文献
110.