Base de dados : MEDLINE
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[PMID]:29402942
[Au] Autor:Kwan CS; Zhao R; Van Hove MA; Cai Z; Leung KC
[Ad] Endereço:Department of Chemistry and Partner State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong.
[Ti] Título:Higher-generation type III-B rotaxane dendrimers with controlling particle size in three-dimensional molecular switching.
[So] Source:Nat Commun;9(1):497, 2018 02 05.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Type III-B rotaxane dendrimers (T3B-RDs) are hyperbranched macromolecules with mechanical bonds on every branching unit. Here we demonstrate the design, synthesis, and characterization of first to third (G1-G3), and up to the fourth (G4) generation (MW > 22,000 Da) of pure organic T3B-RDs and dendrons through the copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. By utilizing multiple molecular shuttling of the mechanical bonds within the sphere-like macromolecule, a collective three-dimensional contract-extend molecular motion is demonstrated by diffusion ordered spectroscopy (DOSY) and atomic force microscopy (AFM). The discrete T3B-RDs are further observed and characterized by AFM, dynamic light scattering (DLS), and mass spectrometry (MS). The binding of chlorambucil and pH-triggered switching of the T3B-RDs are also characterized by H-NMR spectroscopy.
[Mh] Termos MeSH primário: Dendrímeros/síntese química
Rotaxanos/síntese química
[Mh] Termos MeSH secundário: Catálise
Cobre/química
Dendrímeros/química
Substâncias Macromoleculares
Modelos Moleculares
Estrutura Molecular
Movimento (Física)
Tamanho da Partícula
Rotaxanos/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Dendrimers); 0 (Macromolecular Substances); 0 (Rotaxanes); 789U1901C5 (Copper)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180207
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-018-02902-z


  2 / 55423 MEDLINE  
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[PMID]:29303261
[Au] Autor:Zhu TT; Zhang Y; Luo XA; Wang SZ; Jia MQ; Chen ZX
[Ad] Endereço:Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University , Hangzhou 310018, China.
[Ti] Título:Difference in Binding of Long- and Medium-Chain Fatty Acids with Serum Albumin: The Role of Macromolecular Crowding Effect.
[So] Source:J Agric Food Chem;66(5):1242-1250, 2018 Feb 07.
[Is] ISSN:1520-5118
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Fatty acids (FAs) are transported by serum albumin in plasma. Studies have been undertaken to address the binding of MCFAs or LCFAs to human plasma albumin (HPA) and bovine serum albumin (BSA) by characterizing the binding affinities. Previous research on FA binding to serum albumin was usually performed in dilute solutions that are not sufficiently concentrated for the interpretation of the significance of the results under normal physiological conditions. How macromolecular crowded media affect fatty acids and bovine serum albumin (BSA) binding remains unknown. In this article, we investigated the mechanism of FA-BSA binding in a polyethylene glycol crowding environment by using thermodynamic and spectroscopic methods. Molecular crowding increased the binding constant for saturated medium-chain fatty acids (MCFAs) but significantly decreased the binding constant for unsaturated long-chain FAs. The binding sites tended to increase in all the cases. Further investigation revealed that crowding media might loosen the structure of BSA, facilitating MCFA-BSA binding. This research is useful for understanding the transportation of FAs by BSA under physiological conditions and may also help to control digestion by the eventual incorporation of macromolecular crowding agents into food formulations.
[Mh] Termos MeSH primário: Ácidos Graxos/química
Ácidos Graxos/metabolismo
Substâncias Macromoleculares/química
Soroalbumina Bovina/metabolismo
[Mh] Termos MeSH secundário: Sítios de Ligação
Polietilenoglicóis/química
Ligação Proteica
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Fatty Acids); 0 (Macromolecular Substances); 27432CM55Q (Serum Albumin, Bovine); 30IQX730WE (Polyethylene Glycols)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180106
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jafc.7b03548


  3 / 55423 MEDLINE  
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[PMID]:29260726
[Au] Autor:Agarwal T; Manjunath GP; Habib F; Lakshmi Vaddavalli P; Chatterji A
[Ad] Endereço:IISER-Pune, 900 NCL Innovation Park, Dr. Homi Bhaba Road, Pune-411008, India.
[Ti] Título:Role of special cross-links in structure formation of bacterial DNA polymer.
[So] Source:J Phys Condens Matter;30(3):034003, 2018 Jan 24.
[Is] ISSN:1361-648X
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Using data from contact maps of the DNA-polymer of Escherichia coli (E. Coli) (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain. Via suitable Monte Carlo simulations, we show that the presence of these cross-links leads to a particular organization of the chain at large (micron) length scales of the DNA. We also investigate the structure of a ring polymer with an equal number of cross-links at random positions along the chain. We find that though the polymer does get organized at the large length scales, the nature of the organization is quite different from the organization observed with cross-links at specific biologically determined positions. We used the contact map of E. Coli bacteria which has around 4.6 million base pairs in a single circular chromosome. In our coarse-grained flexible ring polymer model, we used 4642 monomer beads and observed that around 80 cross-links are enough to induce the large-scale organization of the molecule accounting for statistical fluctuations caused by thermal energy. The length of a DNA chain even of a simple bacterial cell such as E. Coli is much longer than typical proteins, hence we avoided methods used to tackle protein folding problems. We define new suitable quantities to identify the large scale structure of a polymer chain with a few cross-links.
[Mh] Termos MeSH primário: DNA Bacteriano/química
DNA/química
Polímeros/química
Dobramento de Proteína
[Mh] Termos MeSH secundário: Pareamento de Bases
Escherichia coli
Substâncias Macromoleculares
Modelos Moleculares
Método de Monte Carlo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Bacterial); 0 (Macromolecular Substances); 0 (Polymers); 9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180209
[Lr] Data última revisão:
180209
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171221
[St] Status:MEDLINE
[do] DOI:10.1088/1361-648X/aa9e66


  4 / 55423 MEDLINE  
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[PMID]:29211988
[Au] Autor:Viswanath S; Chemmama IE; Cimermancic P; Sali A
[Ad] Endereço:Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California. Electronic address: shruthi@salilab.org.
[Ti] Título:Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures.
[So] Source:Biophys J;113(11):2344-2353, 2017 Dec 05.
[Is] ISSN:1542-0086
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Modeling of macromolecular structures involves structural sampling guided by a scoring function, resulting in an ensemble of good-scoring models. By necessity, the sampling is often stochastic, and must be exhaustive at a precision sufficient for accurate modeling and assessment of model uncertainty. Therefore, the very first step in analyzing the ensemble is an estimation of the highest precision at which the sampling is exhaustive. Here, we present an objective and automated method for this task. As a proxy for sampling exhaustiveness, we evaluate whether two independently and stochastically generated sets of models are sufficiently similar. The protocol includes testing 1) convergence of the model score, 2) whether model scores for the two samples were drawn from the same parent distribution, 3) whether each structural cluster includes models from each sample proportionally to its size, and 4) whether there is sufficient structural similarity between the two model samples in each cluster. The evaluation also provides the sampling precision, defined as the smallest clustering threshold that satisfies the third, most stringent test. We validate the protocol with the aid of enumerated good-scoring models for five illustrative cases of binary protein complexes. Passing the proposed four tests is necessary, but not sufficient for thorough sampling. The protocol is general in nature and can be applied to the stochastic sampling of any set of models, not just structural models. In addition, the tests can be used to stop stochastic sampling as soon as exhaustiveness at desired precision is reached, thereby improving sampling efficiency; they may also help in selecting a model representation that is sufficiently detailed to be informative, yet also sufficiently coarse for sampling to be exhaustive.
[Mh] Termos MeSH primário: Substâncias Macromoleculares/química
Modelos Moleculares
[Mh] Termos MeSH secundário: Análise por Conglomerados
Processos Estocásticos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Macromolecular Substances)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180120
[Lr] Data última revisão:
180120
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171207
[St] Status:MEDLINE


  5 / 55423 MEDLINE  
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[PMID]:27776769
[Au] Autor:Wheate NJ; Dickson KA; Kim RR; Nematollahi A; Macquart RB; Kayser V; Yu G; Church WB; Marsh DJ
[Ad] Endereço:Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia. Electronic address: nial.wheate@sydney.edu.au.
[Ti] Título:Host-Guest Complexes of Carboxylated Pillar[n]arenes With Drugs.
[So] Source:J Pharm Sci;105(12):3615-3625, 2016 Dec.
[Is] ISSN:1520-6017
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Pillar[n]arenes are a new family of nanocapsules that have shown application in a number of areas, but because of their poor water solubility their biomedical applications are limited. Recently, a method of synthesizing water-soluble pillar[n]arenes was developed. In this study, carboxylated pillar[n]arenes (WP[n], n = 6 or 7) have been examined for their ability to form host-guest complexes with compounds relevant to drug delivery and biodiagnostic applications. Both pillar[n]arenes form host-guest complexes with memantine, chlorhexidine hydrochloride, and proflavine by H nuclear magnetic resonance and modeling. Binding is stabilized by hydrophobic effects within the cavities, and hydrogen bonding and electrostatic interactions at the portals. Encapsulation within WP[6] results in the complete and efficient quenching of proflavine fluorescence, giving rise to "on" and "off" states that have potential in biodiagnostics. The toxicity of the pillar[n]arenes was examined using in vitro growth assays with the OVCAR-3 and HEK293 cell lines. The pillar[n]arenes are relatively nontoxic to cells except at high doses and after prolonged continuous exposure. Overall, the results show that there could be a potentially large range of medical applications for carboxylated pillar[n]arene nanocapsules.
[Mh] Termos MeSH primário: Substâncias Macromoleculares/metabolismo
Modelos Moleculares
Preparações Farmacêuticas/metabolismo
Compostos de Amônio Quaternário/metabolismo
[Mh] Termos MeSH secundário: Células HEK293
Seres Humanos
Substâncias Macromoleculares/química
Memantina/metabolismo
Preparações Farmacêuticas/química
Proflavina/química
Proflavina/metabolismo
Compostos de Amônio Quaternário/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Macromolecular Substances); 0 (Pharmaceutical Preparations); 0 (Quaternary Ammonium Compounds); CY3RNB3K4T (Proflavine); W8O17SJF3T (Memantine)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171201
[Lr] Data última revisão:
171201
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE


  6 / 55423 MEDLINE  
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[PMID]:28991891
[Au] Autor:Herzik MA; Wu M; Lander GC
[Ad] Endereço:Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
[Ti] Título:Achieving better-than-3-Å resolution by single-particle cryo-EM at 200 keV.
[So] Source:Nat Methods;14(11):1075-1078, 2017 Nov.
[Is] ISSN:1548-7105
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Nearly all single-particle cryo-EM structures resolved to better than 4-Å resolution have been determined using 300-keV transmission electron microscopes (TEMs). We demonstrate that it is possible to obtain reconstructions of macromolecular complexes of different sizes to better than 3-Å resolution using a 200-keV TEM. These structures are of sufficient quality to unambiguously assign amino acid rotameric conformations and identify ordered water molecules.
[Mh] Termos MeSH primário: Microscopia Crioeletrônica/métodos
Substâncias Macromoleculares/química
[Mh] Termos MeSH secundário: Limite de Detecção
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Macromolecular Substances)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171111
[Lr] Data última revisão:
171111
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171010
[St] Status:MEDLINE
[do] DOI:10.1038/nmeth.4461


  7 / 55423 MEDLINE  
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[PMID]:28977640
[Au] Autor:Galganski L; Urbanek MO; Krzyzosiak WJ
[Ad] Endereço:Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
[Ti] Título:Nuclear speckles: molecular organization, biological function and role in disease.
[So] Source:Nucleic Acids Res;45(18):10350-10368, 2017 Oct 13.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, were discovered as sites for splicing factor storage and modification. Further studies on transcription and mRNA maturation and export revealed a more general role for splicing speckles in RNA metabolism. Here, we discuss the functional implications of the localization of numerous proteins crucial for epigenetic regulation, chromatin organization, DNA repair and RNA modification to nuclear speckles. We highlight recent advances suggesting that NSs facilitate integrated regulation of gene expression. In addition, we consider the influence of abundant regulatory and signaling proteins, i.e. protein kinases and proteins involved in protein ubiquitination, phosphoinositide signaling and nucleoskeletal organization, on pre-mRNA synthesis and maturation. While many of these regulatory proteins act within NSs, direct evidence for mRNA metabolism events occurring in NSs is still lacking. NSs contribute to numerous human diseases, including cancers and viral infections. In addition, recent data have demonstrated close relationships between these structures and the development of neurological disorders.
[Mh] Termos MeSH primário: Núcleo Celular/metabolismo
Cromatina
Doença/genética
Substâncias Macromoleculares
Proteínas Nucleares
Precursores de RNA/metabolismo
Proteínas de Ligação a RNA/fisiologia
[Mh] Termos MeSH secundário: Cromatina/química
Cromatina/metabolismo
Epigênese Genética/fisiologia
Seres Humanos
Interfase/fisiologia
Substâncias Macromoleculares/química
Substâncias Macromoleculares/metabolismo
Microscopia de Fluorescência
Proteínas Nucleares/química
Proteínas Nucleares/genética
Proteínas Nucleares/metabolismo
Processamento de RNA/genética
Proteínas de Ligação a RNA/química
Proteínas de Ligação a RNA/genética
Proteínas de Ligação a RNA/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Chromatin); 0 (Macromolecular Substances); 0 (Nuclear Proteins); 0 (RNA Precursors); 0 (RNA-Binding Proteins)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171031
[Lr] Data última revisão:
171031
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171005
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx759


  8 / 55423 MEDLINE  
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[PMID]:28924915
[Au] Autor:Meinecke L
[Ad] Endereço:Department of Information Technology, Uppsala University, Uppsala, Sweden. lina.meinecke@uci.edu.
[Ti] Título:Multiscale Modeling of Diffusion in a Crowded Environment.
[So] Source:Bull Math Biol;79(11):2672-2695, 2017 Nov.
[Is] ISSN:1522-9602
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of biological systems, which becomes important in the low copy number regime. To model diffusion in the crowded cell environment efficiently, we compute the jump rates in this mesoscopic model from local first exit times, which account for the microscopic positions of the crowding molecules, while the diffusing molecules jump on a coarser Cartesian grid. We then extract a macroscopic description from the resulting jump rates, where the excluded volume effect is modeled by a diffusion equation with space-dependent diffusion coefficient. The crowding molecules can be of arbitrary shape and size, and numerical experiments demonstrate that those factors together with the size of the diffusing molecule play a crucial role on the magnitude of the decrease in diffusive motion. When correcting the reaction rates for the altered diffusion we can show that molecular crowding either enhances or inhibits chemical reactions depending on local fluctuations of the obstacle density.
[Mh] Termos MeSH primário: Modelos Biológicos
[Mh] Termos MeSH secundário: Simulação por Computador
Difusão
Cinética
Substâncias Macromoleculares/metabolismo
Conceitos Matemáticos
Processos Estocásticos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Macromolecular Substances)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171113
[Lr] Data última revisão:
171113
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170920
[St] Status:MEDLINE
[do] DOI:10.1007/s11538-017-0346-6


  9 / 55423 MEDLINE  
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[PMID]:28923826
[Au] Autor:Redzej A; Ukleja M; Connery S; Trokter M; Felisberto-Rodrigues C; Cryar A; Thalassinos K; Hayward RD; Orlova EV; Waksman G
[Ad] Endereço:Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, London, UK.
[Ti] Título:Structure of a VirD4 coupling protein bound to a VirB type IV secretion machinery.
[So] Source:EMBO J;36(20):3080-3095, 2017 Oct 16.
[Is] ISSN:1460-2075
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Type IV secretion (T4S) systems are versatile bacterial secretion systems mediating transport of protein and/or DNA T4S systems are generally composed of 11 VirB proteins and 1 VirD protein (VirD4). The VirB1-11 proteins assemble to form a secretion machinery and a pilus while the VirD4 protein is responsible for substrate recruitment. The structure of VirD4 in isolation is known; however, its structure bound to the VirB1-11 apparatus has not been determined. Here, we purify a T4S system with VirD4 bound, define the biochemical requirements for complex formation and describe the protein-protein interaction network in which VirD4 is involved. We also solve the structure of this complex by negative stain electron microscopy, demonstrating that two copies of VirD4 dimers locate on both sides of the apparatus, in between the VirB4 ATPases. Given the central role of VirD4 in type IV secretion, our study provides mechanistic insights on a process that mediates the dangerous spread of antibiotic resistance genes among bacterial populations.
[Mh] Termos MeSH primário: Agrobacterium tumefaciens/ultraestrutura
Substâncias Macromoleculares/isolamento & purificação
Substâncias Macromoleculares/ultraestrutura
Sistemas de Secreção Tipo IV/isolamento & purificação
Sistemas de Secreção Tipo IV/ultraestrutura
[Mh] Termos MeSH secundário: Agrobacterium tumefaciens/genética
Conjugação Genética
Microscopia Eletrônica de Transmissão
Mapas de Interação de Proteínas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Macromolecular Substances); 0 (Type IV Secretion Systems)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171020
[Lr] Data última revisão:
171020
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170920
[St] Status:MEDLINE
[do] DOI:10.15252/embj.201796629


  10 / 55423 MEDLINE  
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[PMID]:28891648
[Au] Autor:Inhester T; Nittinger E; Sommer K; Schmidt P; Bietz S; Rarey M
[Ad] Endereço:ZBH - Center for Bioinformatics, Universität Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany.
[Ti] Título:NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures.
[So] Source:J Chem Inf Model;57(9):2132-2142, 2017 Sep 25.
[Is] ISSN:1549-960X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Noncovalent interactions play an important role in macromolecular complexes. The assessment of molecular interactions is often based on knowledge derived from statistics on structural data. Within the last years, the available data in the Brookhaven Protein Data Bank has increased dramatically, quantitatively as well as qualitatively. This development allows the derivation of enhanced interaction models and motivates new ways of data analysis. Here, we present a method to facilitate the analysis of noncovalent interactions enabling detailed insights into the nature of molecular interactions. The method is integrated into a highly variable framework enabling the adaption to user-specific requirements. NAOMInova, the user interface for our method, allows the generation of specific statistics with respect to the chemical environment of substructures. The substructures as well as the analyzed set of protein structures can be chosen arbitrarily. Although NAOMInova was primarily made for data exploration in protein-ligand crystal structures, it can be used in combination with any structure collection, for example, analysis of a carbonyl in the neighborhood of an aromatic ring on a set of structures resulting from a MD simulation. Additionally, a filter for different atom attributes can be applied including the experimental support by electron density for single atoms. In this publication, we present the underlying algorithmic techniques of our method and show application examples that demonstrate NAOMInova's ability to support individual analysis of noncovalent interactions in protein structures. NAOMInova is available at http://www.zbh.uni-hamburg.de/naominova .
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Substâncias Macromoleculares/química
Substâncias Macromoleculares/metabolismo
Interface Usuário-Computador
[Mh] Termos MeSH secundário: Gráficos por Computador
Modelos Moleculares
Conformação Molecular
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Macromolecular Substances)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171010
[Lr] Data última revisão:
171010
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170912
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jcim.7b00291



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