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  • 2010-2014  (201)
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  • 1
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    Global climate evolution during the last deglaciation [Earth, Atmospheric, and Planetary Sciences] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-05-09
    Description: Deciphering the evolution of global climate from the end of the Last Glacial Maximum approximately 19 ka to the early Holocene 11 ka presents an outstanding opportunity for understanding the transient response of Earth’s climate system to external and internal forcings. During this interval of global warming, the decay of ice sheets caused global mean sea level to rise by approximately 80 m; terrestrial and marine ecosystems experienced large disturbances and range shifts; perturbations to the carbon cycle resulted in a net release of the greenhouse gases CO2 and CH4 to the atmosphere; and changes in atmosphere and ocean circulation affected the global distribution and fluxes of water and heat. Here we summarize a major effort by the paleoclimate research community to characterize these changes through the development of well-dated, high-resolution records of the deep and intermediate ocean as well as surface climate. Our synthesis indicates that the superposition of two modes explains much of the variability in regional and global climate during the last deglaciation, with a strong association between the first mode and variations in greenhouse gases, and between the second mode and variations in the Atlantic meridional overturning circulation.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    The development of seasonal tree water deficit in Callitris intratropica (2011)
    Oxford University Press
    Details
    Publication Date: 2011-11-24
    Description: The tropical conifer Callitris intratropica (Cupressaceae) produces clear annual growth rings, and has been shown to be potentially useful for understanding past climate variability in northern Australia. As climate patterns in this region become less predictable, an understanding of plant responses to different weather patterns is of importance. In this paper, we examine tree water relations using a parameter here called tree water deficit ( D ), determined from de-trended stem size variability in densely grown (‘grove’) and isolated trees. This parameter provides an integrated measure of the trees' response to water supply and demand under constantly changing environmental conditions. The work, conducted over 12 months, found that daily variation in tree water deficit was determined mainly by soil water availability, but temperature and relative humidity contributed more to the variability over some periods. Isolated and grove trees exhibited quite distinct patterns of D development during the year, but particularly during the transition between the dry and wet seasons. The results of this work suggest that the dendrochronological interpretation of tree rings in the context of strongly seasonal water availability should incorporate an understanding of the development of seasonal drought in isolated trees compared with trees experiencing strong intra-specific competition. Different responses based on the ecological situations of the trees will affect their patterns of stem growth, and ultimately the climatic information that is incorporated in ring width variability.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 3
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    RNA polymerase and transcription elongation factor Spt4/5 complex structure [Biochemistry] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-01-12
    Description: Spt4/5 in archaea and eukaryote and its bacterial homolog NusG is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating RNA polymerase. Here, we present the crystal structure of Spt4/5 as well as the structure of RNA polymerase-Spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. The Spt4/5 binds in the middle of RNA polymerase claw and encloses the DNA, reminiscent of the DNA polymerase clamp and ring helicases. The transcription elongation complex model reveals that the Spt4/5 is an upstream DNA holder and contacts the nontemplate DNA in the transcription bubble. These structures reveal that the cellular RNA polymerases also use a strategy of encircling DNA to enhance its processivity as commonly observed for many nucleic acid processing enzymes including DNA polymerases and helicases.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Rolling-Circle Transposons Catalyze Genomic Innovation in a Mammalian Lineage (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-08
    Description: Rolling-circle transposons ( Helitrons ) are a newly discovered group of mobile DNA widespread in plant and invertebrate genomes but limited to the bat family Vespertilionidae among mammals. Little is known about the long-term impact of Helitron activity because the genomes where Helitron activity has been extensively studied are predominated by young families. Here, we report a comprehensive catalog of vetted Helitrons from the 7 x Myotis lucifugus genome assembly. To estimate the timing of transposition, we scored presence/absence across related vespertilionid genome sequences with estimated divergence times. This analysis revealed that the Helibat family has been a persistent source of genomic innovation throughout the vespertilionid diversification from approximately 30–36 Ma to as recently as approximately 1.8–6 Ma. This is the first report of persistent Helitron transposition over an extended evolutionary timeframe. These findings illustrate that the pattern of Helitron activity is akin to the vertical persistence of LINE retrotransposons in primates and other mammalian lineages. Like retrotransposition in primates, rolling-circle transposition has generated lineage-specific variation and accounts for approximately 110 Mb, approximately 6% of the genome of M. lucifugus . The Helitrons carry a heterogeneous assortment of host sequence including retroposed messenger RNAs, retrotransposons, DNA transposons, as well as introns, exons and regulatory regions (promoters, 5'-untranslated regions [UTRs], and 3'-UTRs) of which some are evolving in a pattern suggestive of purifying selection. Evidence that Helitrons have contributed putative promoters, exons, splice sites, polyadenylation sites, and microRNA-binding sites to transcripts otherwise conserved across mammals is presented, and the implication of Helitron activity to innovation in these unique mammals is discussed.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    PUMA-MCL-1 folding and binding mechanism [Biophysics and Computational Biology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-10-29
    Description: Protein–protein interactions are at the heart of regulatory and signaling processes in the cell. In many interactions, one or both proteins are disordered before association. However, this disorder in the unbound state does not prevent many of these proteins folding to a well-defined, ordered structure in the bound state. Here...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    The Anatomy of a Buried Submarine Hydrothermal System, Clark Volcano, Kermadec Arc, New Zealand (2014)
    Society of Economic Geologists (SEG)
    Details
    Publication Date: 2014-10-31
    Description: Clark volcano of the Kermadec arc, northeast of New Zealand, is a large stratovolcano comprised of two coalescing volcanic cones; an apparently younger, more coherent, twin-peaked edifice to the northwest and a relatively older, more degraded and tectonized cone to the southeast. High-resolution water column surveys show an active hydrothermal system at the summit of the NW cone largely along a ridge spur connecting the two peaks, with activity also noted at the head of scarps related to sector collapse. Clark is the only known cone volcano along the Kermadec arc to host sulfide mineralization. Volcano-scale gravity and magnetic surveys over Clark show that it is highly magnetized, and that a strong gravity gradient exists between the two edifices. Modeling suggests that a crustal-scale fault lies between these two edifices, with thinner crust beneath the NW cone. Locations of regional earthquake epicenters show a southwest-northeast trend bisecting the two Clark cones, striking northeastward into Tangaroa volcano. Detailed mapping of magnetics above the NW cone summit shows a highly magnetized "ring structure" ~350 m below the summit that is not apparent in the bathymetry; we believe this structure represents the top of a caldera. Oblate zones of low (weak) magnetization caused by hydrothermal fluid upflow, here termed "burn holes," form a pattern in the regional magnetization resembling Swiss cheese. Presumably older burn holes occupy the inner margin of the ring structure and show no signs of hydrothermal activity, while younger burn holes are coincident with active venting on the summit. A combination of mineralogy, geochemistry, and seafloor mapping of the NW cone shows that hydrothermal activity today is largely manifest by widespread diffuse venting, with temperatures ranging between 56° and 106°C. Numerous, small (≤30 cm high) chimneys populate the summit area, with one site host to the ~7-m-tall "Twin Towers" chimneys with maximum vent fluid temperatures of 221°C (pH 4.9), consistent with 34 S anhydrite-pyrite values indicating formation temperatures of ~228° to 249°C. Mineralization is dominated by pyrite-marcasite-barite-anhydrite. Radiometric dating using the 228 Ra/ 226 Ra and 226 Ra/Ba methods shows active chimneys to be 〈20 with most 〈2 years old. However, the chimneys at Clark show evidence for mixing with, and remobilizing of, barite as old as 19,000 years. This is consistent with Nd and Sr isotope compositions of Clark chimney and sulfate crust samples that indicate mixing of ~40% seawater with a vent fluid derived from low K lavas. Similarly, REE data show the hydrothermal fluids have interacted with a plagioclase-rich source rock. A holistic approach to the study of the Clark hydrothermal system has revealed a two-stage process whereby a caldera-forming volcanic event preceded a later cone-building event. This ensured a protracted (at least 20 ka yrs) history of hydrothermal activity and associated mineral deposition. If we assume at least 200-m-high walls for the postulated (buried) caldera, then hydrothermal fluids would have exited the seafloor 20 ka years ago at least 550 m deeper than they do today, with fluid discharge temperatures potentially much hotter (~350°C). Subsequent to caldera infilling, relatively porous volcaniclastic and other units making up the cone acted as large-scale filters, enabling ascending hydrothermal fluids to boil and mix with seawater subseafloor, effectively removing the metals (including remobilized Cu) in solution before they reached the seafloor. This has implications for estimates for the metal inventory of seafloor hydrothermal systems pertaining to arc hydrothermal systems.
    Print ISSN: 0361-0128
    Topics: Geosciences
    Published by Society of Economic Geologists (SEG)
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  • 7
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    Predicting protein structures with a multiplayer online game (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-08-06
    Description: People exert large amounts of problem-solving effort playing computer games. Simple image- and text-recognition tasks have been successfully 'crowd-sourced' through games, but it is not clear if more complex scientific problems can be solved with human-directed computing. Protein structure prediction is one such problem: locating the biologically relevant native conformation of a protein is a formidable computational challenge given the very large size of the search space. Here we describe Foldit, a multiplayer online game that engages non-scientists in solving hard prediction problems. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy. We show that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms; unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956414/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooper, Seth -- Khatib, Firas -- Treuille, Adrien -- Barbero, Janos -- Lee, Jeehyung -- Beenen, Michael -- Leaver-Fay, Andrew -- Baker, David -- Popovic, Zoran -- Players, Foldit -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Aug 5;466(7307):756-60. doi: 10.1038/nature09304.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20686574" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Computational Biology/*methods ; Computer Graphics ; Computer Simulation ; Cooperative Behavior ; Cues ; *Games, Experimental ; *Group Processes ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Imaging, Three-Dimensional ; *Internet ; Leisure Activities ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Photic Stimulation ; *Problem Solving ; Protein Conformation ; *Protein Folding ; Proteins/*chemistry/metabolism ; Stochastic Processes ; Thermodynamics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Quantitative reactivity profiling predicts functional cysteines in proteomes (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-11-19
    Description: Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here we describe a proteomics method to profile quantitatively the intrinsic reactivity of cysteine residues en masse directly in native biological systems. Hyper-reactivity was a rare feature among cysteines and it was found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyper-reactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and is involved in iron-sulphur protein biogenesis. We also demonstrate that quantitative reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058684/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058684/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weerapana, Eranthie -- Wang, Chu -- Simon, Gabriel M -- Richter, Florian -- Khare, Sagar -- Dillon, Myles B D -- Bachovchin, Daniel A -- Mowen, Kerri -- Baker, David -- Cravatt, Benjamin F -- CA087660/CA/NCI NIH HHS/ -- MH084512/MH/NIMH NIH HHS/ -- R01 CA087660/CA/NCI NIH HHS/ -- R01 CA087660-09/CA/NCI NIH HHS/ -- R01 GM085117/GM/NIGMS NIH HHS/ -- R01 GM090294/GM/NIGMS NIH HHS/ -- R01 GM090294-02/GM/NIGMS NIH HHS/ -- R37 CA087660/CA/NCI NIH HHS/ -- R37 CA087660-10/CA/NCI NIH HHS/ -- U54 MH084512/MH/NIMH NIH HHS/ -- U54 MH084512-030004/MH/NIMH NIH HHS/ -- England -- Nature. 2010 Dec 9;468(7325):790-5. doi: 10.1038/nature09472. Epub 2010 Nov 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21085121" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biocatalysis ; Cell Line, Tumor ; Conserved Sequence ; Cysteine/analysis/*metabolism ; Humans ; Hydrolases/chemistry/metabolism ; Iron-Sulfur Proteins/biosynthesis ; Liver/metabolism ; Mice ; Myocardium/metabolism ; Nuclear Proteins/chemistry/metabolism ; Oxidation-Reduction ; Protein Engineering ; Protein Hydrolysates ; Protein-Arginine N-Methyltransferases/chemistry/metabolism ; Proteins/*chemistry/*metabolism ; Proteome/*chemistry/*metabolism ; Proteomics/methods ; Repressor Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-22
    Description: The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241958/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241958/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siegel, Justin B -- Zanghellini, Alexandre -- Lovick, Helena M -- Kiss, Gert -- Lambert, Abigail R -- St Clair, Jennifer L -- Gallaher, Jasmine L -- Hilvert, Donald -- Gelb, Michael H -- Stoddard, Barry L -- Houk, Kendall N -- Michael, Forrest E -- Baker, David -- R01 GM075962/GM/NIGMS NIH HHS/ -- T32 GM008268/GM/NIGMS NIH HHS/ -- T32 GM008268-24/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):309-13. doi: 10.1126/science.1190239.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20647463" target="_blank"〉PubMed〈/a〉
    Keywords: Acrylamides/chemistry ; Algorithms ; Butadienes/chemistry ; Carbon/*chemistry ; Catalysis ; Catalytic Domain ; Computer Simulation ; *Computer-Aided Design ; Crystallography, X-Ray ; Enzymes/*chemistry/genetics ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Mutagenesis ; Physicochemical Processes ; Protein Conformation ; *Protein Engineering ; Proteins/*chemistry/genetics ; Software ; Stereoisomerism ; Substrate Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    NMR structure determination for larger proteins using backbone-only data (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-06
    Description: Conventional protein structure determination from nuclear magnetic resonance data relies heavily on side-chain proton-to-proton distances. The necessary side-chain resonance assignment, however, is labor intensive and prone to error. Here we show that structures can be accurately determined without nuclear magnetic resonance (NMR) information on the side chains for proteins up to 25 kilodaltons by incorporating backbone chemical shifts, residual dipolar couplings, and amide proton distances into the Rosetta protein structure modeling methodology. These data, which are too sparse for conventional methods, serve only to guide conformational search toward the lowest-energy conformations in the folding landscape; the details of the computed models are determined by the physical chemistry implicit in the Rosetta all-atom energy function. The new method is not hindered by the deuteration required to suppress nuclear relaxation processes for proteins greater than 15 kilodaltons and should enable routine NMR structure determination for larger proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909653/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909653/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raman, Srivatsan -- Lange, Oliver F -- Rossi, Paolo -- Tyka, Michael -- Wang, Xu -- Aramini, James -- Liu, Gaohua -- Ramelot, Theresa A -- Eletsky, Alexander -- Szyperski, Thomas -- Kennedy, Michael A -- Prestegard, James -- Montelione, Gaetano T -- Baker, David -- GM76222/GM/NIGMS NIH HHS/ -- P41 GM103390/GM/NIGMS NIH HHS/ -- R01 GM092802/GM/NIGMS NIH HHS/ -- R01 GM095693/GM/NIGMS NIH HHS/ -- RR005351/RR/NCRR NIH HHS/ -- U54 GM074958/GM/NIGMS NIH HHS/ -- U54 GM074958-05/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Feb 19;327(5968):1014-8. doi: 10.1126/science.1183649. Epub 2010 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20133520" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; Models, Molecular ; Monte Carlo Method ; Nuclear Magnetic Resonance, Biomolecular/*methods ; *Protein Conformation ; Protein Folding ; Proteins/*chemistry ; Software ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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