Modeling complex molecular interactions involving proteins and DNA.

Abstract:

:We have presented a perspective of progress in three areas of simulations of complex molecules: the development of force fields for molecular simulation; the application of computer graphics, molecular mechanics and molecular dynamics in simulations of DNA and DNA-drug complexes and the application of computer graphics, molecular mechanics and quantum mechanics in studies of enzyme substrate interactions. It is our perspective that improvements are being made in force fields, and these will allow a more accurate simulation of structures and energies of complex molecules. In the area of DNA molecular mechanics and dynamics, it is clear that the use of computer graphics model building combined with NMR NOE data is a potentially very powerful tool in accurately determining structures of drug-DNA complexes using molecular mechanics and dynamics. Finally, we are in a position to reasonably simulate structures and (qualitatively) energies for complete reaction pathways of enzymes using a combination of computer graphics, molecular mechanics and quantum mechanics. More accurate energies and pathways are sure to follow, using the combined molecular mechanics/quantum mechanics optimization developed by Singh and the free energy perturbation methods pioneered in Groningen and Houston.

journal_name

Ann N Y Acad Sci

authors

Kollman PA,Weiner S,Seibel G,Lybrand T,Singh UC,Caldwell J,Rao SN

doi

10.1111/j.1749-6632.1986.tb20954.x

subject

Has Abstract

pub_date

1986-01-01 00:00:00

pages

234-44

eissn

0077-8923

issn

1749-6632

journal_volume

482

pub_type

杂志文章
  • The porous boundaries between explicit and implicit memory: behavioral and neural evidence.

    abstract::Explicit memory refers to the conscious retrieval of past information or experiences, whereas implicit memory refers to an unintentional or nonconscious form of retrieval. Much of the literature in cognitive psychology and cognitive neuroscience has focused on differences between explicit and implicit memory, and the ...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1111/j.1749-6632.2010.05946.x

    authors: Dew ITZ,Cabeza R

    更新日期:2011-04-01 00:00:00

  • Effects of chronic maternal ethanol exposure on hippocampal and striatal morphology in offspring.

    abstract::Astrocytes and serotoninergic neurons play a role in central nervous system (CNS) development, probably through serotonin (5HT) stimulation of the glial 5HT(1A) receptor. Activation of 5HT(1A) receptors causes the release of S-100 beta, a glial derived growth factor. In vitro, astrocytes are profoundly altered by chro...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.2002.tb04176.x

    authors: Ramos AJ,Evrard SG,Tagliaferro P,Tricárico MV,Brusco A

    更新日期:2002-06-01 00:00:00

  • Molecular mechanism of metabolic syndrome X: contribution of adipocytokines adipocyte-derived bioactive substances.

    abstract::Syndrome X is a clinical syndrome in which multiple risks cluster in an individual, and it is a common basis of vascular disease in the industrial countries. The molecular basis of Syndrome X, however, has not been elucidated. We have analyzed body fat distribution using CT scan and have shown that people who have acc...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1111/j.1749-6632.1999.tb07793.x

    authors: Matsuzawa Y,Funahashi T,Nakamura T

    更新日期:1999-11-18 00:00:00

  • Pool film boiling experiments on a wire in low gravity: preliminary results.

    abstract::This paper reports preliminary results for pool film boiling on a wire immersed in almost saturated FC72 recently obtained during an experimental campaign performed in low gravity on the European Space Agency Zero-G airplane, (reduced gravity level 10(-2)). This is part of a long-term research program on the effect of...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.2002.tb05923.x

    authors: Di Marco P,Grassi W,Trentavizi F

    更新日期:2002-10-01 00:00:00

  • The importance of scientific collecting and natural history museums for comparative neuroanatomy.

    abstract::The comparative study of vertebrate brains is inherently dependent upon access to a sufficient number of species and specimens to perform meaningful comparisons. Although many studies rely on compiling published information, continued specimen collection, in addition to more extensive use of existing brain collections...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1111/j.1749-6632.2011.05977.x

    authors: Iwaniuk AN

    更新日期:2011-05-01 00:00:00

  • The role of input-output analysis of energy and ecologic systems. In the early development of ecological economics--a personal perspective.

    abstract::A summary is provided of the early history of research on the flow of nonrenewable energy resources through the economy and of the flow of renewable energy resources through a natural ecosystem. The techniques are similar, and many specific applications are provided. A combined economic and ecological technique is als...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.2009.05165.x

    authors: Hannon B

    更新日期:2010-01-01 00:00:00

  • Mechanisms by which dopamine receptors may influence synaptic plasticity.

    abstract::While dopamine (DA) receptors mediate acute effects of amphetamine and cocaine, chronic drug administration produces many glutamate-dependent adaptations, including LTP in reward-related neuronal circuits. An important question presents itself: How do DA receptors influence glutamate-dependent synaptic plasticity? Alt...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1196/annals.1300.015

    authors: Wolf ME,Mangiavacchi S,Sun X

    更新日期:2003-11-01 00:00:00

  • Carnitines and its congeners: a metabolic pathway to the regulation of immune response and inflammation.

    abstract::Carnitine and its congeners may regulate the immune networks, and their influence on functions of immune cells predominantly or exclusively relies on carnitine-dependent energy production from fatty acids. A reduced pool of carnitines has been demonstrated in either serum or tissues, or both, from patients with a wide...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1196/annals.1320.012

    authors: Famularo G,De Simone C,Trinchieri V,Mosca L

    更新日期:2004-11-01 00:00:00

  • The pivotal role of iron in NF-kappa B activation and nigrostriatal dopaminergic neurodegeneration. Prospects for neuroprotection in Parkinson's disease with iron chelators.

    abstract::R-Apomorphine (APO) the catechol-derived dopamine D1-D2 receptor agonist has been shown to be highly potent iron chelator and radical scavenger and inhibitor of membrane lipid peroxidation in vitro, in vivo and in cell culture employing PC12 cells. Its potency has been compared to the prototype iron chelator desferrio...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.1999.tb07977.x

    authors: Youdim MB,Grünblatt E,Mandel S

    更新日期:1999-01-01 00:00:00

  • Development of ipilimumab: a novel immunotherapeutic approach for the treatment of advanced melanoma.

    abstract::The immunotherapeutic agent ipilimumab has helped address a significant unmet need in the treatment of advanced melanoma. Ipilimumab is a fully human monoclonal antibody that targets cytotoxic T-lymphocyte antigen-4 (CTLA-4), thereby augmenting antitumor immune responses. After decades in which a number of clinical tr...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1111/nyas.12180

    authors: Wolchok JD,Hodi FS,Weber JS,Allison JP,Urba WJ,Robert C,O'Day SJ,Hoos A,Humphrey R,Berman DM,Lonberg N,Korman AJ

    更新日期:2013-07-01 00:00:00

  • Fatty acid composition in fractions of structural and storage lipids in liver and skeletal muscle of hereditary hypertriglyceridemic rats.

    abstract::The fatty acid (FA) compositions of liver and skeletal muscle structural lipids, overall phospholipids and phosphatidylcholine, and triglycerides (TG) were determined in the hereditary hypertriglyceridemic (HTG) rat, a nonobese animal model of the insulin resistance syndrome. Four groups of HTG rats and four groups of...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.1997.tb51860.x

    authors: Bohov P,Seböková E,Gasperíková D,Langer P,Klimes I

    更新日期:1997-09-20 00:00:00

  • Calorie restriction, post-reproductive life span, and programmed aging: a plea for rigor.

    abstract::All scientists are acutely aware of the profound challenge that they face when communicating scientific findings to nonscientists, especially when great uncertainty is involved and when the topic is of personal interest to the general public. Simplification of the issues--sometimes extending to a degree of oversimplif...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1196/annals.1404.029

    authors: De Grey AD

    更新日期:2007-11-01 00:00:00

  • Dendritic cell-based proliferative assays of peripheral T cell responses to tetanus toxoid.

    abstract::Antigen-specific proliferative responses of peripheral blood T cells are widely used in humans to study the T cell compartment. However, responses to autoantigens are often weak and poorly reproducible. Here we show, using a test recall antigen (tetanus toxoid), that absolute levels of proliferation, minimally detecta...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.2002.tb02963.x

    authors: Narendran P,Elsegood K,Leech NJ,Dayan CM

    更新日期:2002-04-01 00:00:00

  • Neuroendocrine responses to hypoglycemia.

    abstract::The counterregulatory response to hypoglycemia is a complex and well-coordinated process. As blood glucose concentration declines, peripheral and central glucose sensors relay this information to central integrative centers to coordinate neuroendocrine, autonomic, and behavioral responses and avert the progression of ...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1111/j.1749-6632.2010.05820.x

    authors: Tesfaye N,Seaquist ER

    更新日期:2010-11-01 00:00:00

  • Ascorbic acid changes in cultured rabbit lenses after microwave irradiation.

    abstract::Whole body exposure of rabbits to microwave radiation causes a decrease in ascorbic acid in the lens. In our study, rabbit lenses maintained in culture medium (37 degrees C) were exposed to either pulsed or continuous wave S-band radiation for 10-15 min at power densities between 0 and 200 mW/cm-2. Total ascorbic acid...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.1975.tb35994.x

    authors: Weiter JJ,Finch ED,Schulz W,Frattali V

    更新日期:1975-02-28 00:00:00

  • The role of primary cilia in obesity and diabetes.

    abstract::One in 12 people worldwide suffers from diabetes and more than 90% of affected adult individuals are diagnosed with type 2 diabetes mellitus (T2DM). Obesity adds to the personal risk to develop T2DM, and both metabolic diseases are rampantly increasing worldwide. Over recent years, primary cilia have moved into the fo...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1111/nyas.13216

    authors: Volta F,Gerdes JM

    更新日期:2017-03-01 00:00:00

  • Ornithine is a novel amino acid and a marker of arginine damage by oxoaldehydes in senescent proteins.

    abstract::Long-lived proteins undergo age-related postsynthetic modifications by glycation and advanced glycation end products (AGEs), which destabilize them by altering their conformation and charge. It was accidentally discovered that ornithine (orn) increased with age in acid hydrolyzates of human skin collagen and lens crys...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1196/annals.1333.015

    authors: Sell DR,Monnier VM

    更新日期:2005-06-01 00:00:00

  • Fluoride in chilies from southwestern china.

    abstract::The purpose of this research is to investigate the fluoride contents in the chilies from southwest China and other countries in order to calculate the difference in fluoride levels in the fresh chilies. The standard method in China for analysis of fluoride in food (GB/T 5009.18-2003) was applied to determinate the flu...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1196/annals.1454.035

    authors: Li B,Li S,Wang M,Liu X,Zheng B

    更新日期:2008-10-01 00:00:00

  • Serological and clinical characterization of anti-dsDNA and anti-PM/Scl double-positive patients.

    abstract::Antibodies to double-stranded desoxyribonucleic acid (dsDNA) and to the polymyositis/scleroderma (PM/Scl) complex are regarded as serological markers for systemic lupus erythematosus (SLE) and PM/Scl overlap syndrome, respectively. In a previous study, serum samples were identified that contained antibodies specific f...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1196/annals.1398.037

    authors: Mahler M,Greidinger EL,Szmyrka M,Kromminga A,Fritzler MJ

    更新日期:2007-08-01 00:00:00

  • Novel selective compounds for the investigation of imidazoline receptors.

    abstract::Over several years our group has sought to synthesize and identify selective ligands for imidazoline (I) receptors, in particular the I2 binding site. As a consequence, [3H]2-(2-benzofuranyl)-2-imidazoline (2BFI) has proved extremely useful for binding and autoradiographic studies. More recently we have synthesized a ...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.1999.tb09344.x

    authors: Hudson AL,Gough R,Tyacke R,Lione L,Lalies M,Lewis J,Husbands S,Knight P,Murray F,Hutson P,Nutt DJ

    更新日期:1999-06-21 00:00:00

  • Multifunctionalized biocompatible microspheres for sensing.

    abstract::We present our achievements in the synthesis and application of multifunctionalized, cross-linked, polystyrene microspheres, which remarkably and quite generally are taken up by all cell types studied to date. Importantly, the nature of these synthetic beads allows multistep solid-phase chemistry and the ability to bi...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1196/annals.1430.004

    authors: Sánchez-Martín RM,Alexander L,Bradley M

    更新日期:2008-01-01 00:00:00

  • Fungal formulations to control Rhipicephalus sanguineus engorged females.

    abstract::Entomopathogenic fungi are promising alternatives to chemical acaricides in controlling tick populations; however, biological formulations are required to improve conidial performance of these pathogens in the field. This study evaluated the effect of in vitro treatment of Rhipicephalus sanguineus with conidial formul...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1196/annals.1428.030

    authors: Reis RC,Fernandes EK,Bittencourt VR

    更新日期:2008-12-01 00:00:00

  • Evolution of alpha-fetoprotein serum levels throughout life in humans and rats, and during pregnancy in the rat.

    abstract::A radioimmunoassay method (RIA) with specific antisera for human and rat alpha fetoprotein (AFP) was used to study the evolution of AFP levels in humans and rats, respectively, throughout the life span. Sera of 66 rats, aged 3-70 weeks, as well as sera of 201 clinically well children, 192 healthy blood donors, and 16...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.1975.tb25398.x

    authors: Masseyeff R,Gilli J,Krebs B,Calluaud A,Bonet C

    更新日期:1975-08-22 00:00:00

  • Hemodynamic-force-induced difference of interendothelial junctional complexes.

    abstract::1. The flow divider of the brachiocephalic branching of the rabbit aorta had both high and low shear stress regions, each of which was covered by endothelial cells with low and high permeability respectively, even in normolipidemic intact rabbits. When rabbits were placed on an atherogenic diet, low shear regions were...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.1994.tb17311.x

    authors: Yoshida Y,Okano M,Wang S,Kobayashi M,Kawasumi M,Hagiwara H,Mitsumata M

    更新日期:1995-01-17 00:00:00

  • Ketoconazole treatment of coccidioidal meningitis.

    abstract::Fifteen patients with coccidioidal meningitis were treated with high doses of ketoconazole for up to 4 years. Five patients were treated with ketoconazole alone. One clinically failed, one developed hepatotoxicity, and three achieved remission of meningitis. One patient received intrathecal AMB in addition to ketocona...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.1988.tb40446.x

    authors: Graybill JR,Stevens DA,Galgiani JN,Sugar AM,Craven PC,Gregg C,Huppert M,Cloud G,Dismukes WE

    更新日期:1988-01-01 00:00:00

  • Biomedical science and the third world. Under the volcano. Epidemiologic problems and prospects.

    abstract::Rapid advances in the biomedical sciences are producing new means of intervention against many of the major tropical diseases. The discovery of new drugs, vaccines and diagnostic tests, however, is only the first, though important, step down an often long and difficult road to their effective deployment in disease con...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1111/j.1749-6632.1989.tb27372.x

    authors: Smith PG

    更新日期:1989-01-01 00:00:00

  • Activity-dependent regulation of GABAA receptors.

    abstract::GABAA receptor heterogeneity is based on the combinatorial assembly of a large family of subunits into distinct receptor subtypes. A neuron-specific expression pattern of receptor subtypes has been demonstrated in adult rat brain, which can be reproduced in vitro in primary neuron cultures. This suggests that genetic ...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.1999.tb11342.x

    authors: Penschuck S,Paysan J,Giorgetta O,Fritschy JM

    更新日期:1999-04-30 00:00:00

  • Neurobiological consequences of early stress and childhood maltreatment: are results from human and animal studies comparable?

    abstract::Recent studies have reported an association between exposure to childhood abuse or neglect and alterations in brain structure or function. One limitation of these studies is that they are correlational and do not provide evidence of a cause-effect relationship. Preclinical studies on the effects of exposure to early l...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1196/annals.1364.024

    authors: Teicher MH,Tomoda A,Andersen SL

    更新日期:2006-07-01 00:00:00

  • Adenylate cyclase in muscular dystrophy.

    abstract::The purpose of this study was to determine whether the previously reported differences in adenylate cyclase activity between the sarcolemma of normal and dystrophic chick muscles are also found in the SR, to search for a possible relationship between the adenylate cyclase changes and the pathophysiology of dystrophy, ...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章

    doi:10.1111/j.1749-6632.1979.tb56587.x

    authors: Rodan GA,Rodan SB,Raible DG,Cutler LS,Wacholtz M,Sha'afi RI

    更新日期:1979-01-01 00:00:00

  • Mechanism of induction of apoptosis by p73 and its relevance to neuroblastoma biology.

    abstract::TP73, as a TP53 homologue, drew the attention of tumor biologists because it is rarely mutated in human cancers and can induce cell cycle arrest and apoptosis by activating genes also regulated by p53. However, TP73 harbors an additional promoter that produces a dominant negative p73 protein (deltaNp73) having the opp...

    journal_title:Annals of the New York Academy of Sciences

    pub_type: 杂志文章,评审

    doi:10.1196/annals.1322.015

    authors: Rossi M,Sayan AE,Terrinoni A,Melino G,Knight RA

    更新日期:2004-12-01 00:00:00