22 p. ; 23 cm
Topic: Biomolecules
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2.0
texts
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Topics: Biochemistry, Biomolecules, Biomolecules -- Structure, Biophysics
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5.0
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x, 176 p. : 28 cm
Topics: Biomolecules -- Analysis -- Congresses, Biomolecules -- Spectra -- Congresses
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3.0
Jul 26, 2020
07/20
by
European Conference on the Spectroscopy of Biological Molecules (5th : 1993 : Loutraki, Greece)
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eye 3
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xvi, 409 p. : 25 cm
Topics: Biomolecules -- Spectra -- Congresses, Biomolecules -- Analysis -- Congresses
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4.0
web
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Biomolecules dumped with WikiTeam tools.
Topics: wiki, wikiteam, wikispaces, Biomolecules, biomolecules, biomolecules.wikispaces.com
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3.0
Jul 14, 2021
07/21
by
NATO Advanced Study Institute on Spectroscopy of Biological Molecules (1983 : Acquafredda di Maratea, Italy)
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eye 3
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x, 646 p. : 25 cm
Topics: Biomolecules -- Spectra -- Congresses, Biomolecules -- Analysis -- Congresses
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7.0
May 2, 2022
05/22
by
Dechow, Frederick J
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eye 7
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x, 490 p. : 25 cm
Topics: Biomolecules -- Separation, Biomolecules -- Purification, Biotechnology -- Technique
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20
May 9, 2020
05/20
by
Schlick, Tamar
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xliii, 634 p. : 25 cm
Topics: Biomolecules -- Models, Biomolecules -- Models -- Computer simulation
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3.0
texts
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vii, 146 p. : 28 cm
Topics: Biomolecules -- Analysis -- Congresses, Biomolecules -- Spectra -- Congresses
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7.0
Jul 27, 2020
07/20
by
Bennett, Thomas Peter
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eye 7
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vi, 186 p. : 24 cm
Topics: Biomolecules, Biochemistry
Click here to view the University of Florida catalog record
Topics: Nanoparticles, Biomolecules
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17
Aug 19, 2015
08/15
by
Collins, W. P
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Includes bibliographies and index
Topics: Immunoassay, Biomolecules
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5.0
Apr 28, 2021
04/21
by
International Symposium on Biomolecular Structure, Conformation, Function, and Evolution (1978 : Madras, India)
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eye 5
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2 v. : 26 cm
Topic: Biomolecules -- Congresses
5
5.0
Feb 8, 2022
02/22
by
Klotz, Irving M. (Irving Myron), 1916-2005
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xiv, 138 p. : 24 cm
Topics: Bioenergetics, Biomolecules
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Oct 16, 2014
10/14
by
Kumosinski, Thomas F; Liebman, Michael N., 1947-; American Chemical Society. Division of Agricultural and Food Chemistry; American Chemical Society. Meeting (205th : 1993 : Denver, Colo.)
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"Developed from a symposium sponsored by the Divison of Agricultural and Food Chemistry at the 205th National Meeting of the American Chemical Society, Denver, Colorado, March 28-April 2, 1993."
Topics: Biomolecules, Proteins
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49
Jun 17, 2010
06/10
by
Bennett, Thomas Peter; Frieden, Earl, joint author
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Includes bibliographies
Topics: Biomolecules, Biochemistry
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5.0
Jun 30, 2018
06/18
by
Annie M. Westerlund; Tyler J. Harpole; Christian Blau; Lucie Delemotte
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A free energy landscape estimation-method based on Bayesian inference is presented and used for comparing the efficiency of thermally enhanced sampling methods with respect to regular molecular dynamics, where the simulations are carried out on two binding states of calmodulin. The proposed free energy estimation method (the GM method) is compared to other estimators using a toy model showing that the GM method provides a robust estimate not subject to overfitting. The continuous nature of the...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1704.00343
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5.0
Jun 30, 2018
06/18
by
B. Amor; S. N. Yaliraki; R. Woscholski; M. Barahona
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Allosteric regulation at distant sites is central to many cellular processes. In particular, allosteric sites in proteins are a major target to increase the range and selectivity of new drugs, and there is a need for methods capable of identifying intra-molecular signalling pathways leading to allosteric effects. Here, we use an atomistic graph-theoretical approach that exploits Markov transients to extract such pathways and exemplify our results in an important allosteric protein, caspase-1....
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1411.2847
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3.0
Jun 30, 2018
06/18
by
Martin Mann; Marcel Kucharik; Christoph Flamm; Michael T. Wolfinger
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Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems, however they are still restricted by huge memory requirements of exact approaches. We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1404.0270
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4.0
Jun 29, 2018
06/18
by
Michael F. Hagan; Roya Zandi
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In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical processes. We present an overview of recent technological and algorithmic developments, which are enabling simulations to describe the large ranges of length-and time-scales relevant to assembly, under conditions more closely matched to experiments than in earlier...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1607.01452
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12
Jun 29, 2018
06/18
by
Bartosz Rozycki; Marek Cieplak
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eye 12
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Cellulosomes are complex multi-enzyme machineries which efficiently degrade plant cell-wall polysaccharides. The multiple domains of the cellulosome proteins are often tethered together by intrinsically disordered regions. The properties and functions of these disordered linkers are not well understood. In this work, we study endoglucanase Cel8A, which is a relevant enzymatic component of the cellulosomes of Clostridium thermocellum. We use both all-atom and coarse-grained simulations to...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1609.07000
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4.0
Jun 30, 2018
06/18
by
Kelin Xia; Guo-Wei Wei
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Persistent homology has emerged as a popular technique for the topological simplification of big data, including biomolecular data. Multidimensional persistence bears considerable promise to bridge the gap between geometry and topology. However, its practical and robust construction has been a challenge. We introduce two families of multidimensional persistence, namely pseudo-multidimensional persistence and multiscale multidimensional persistence. The former is generated via the repeated...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1412.7679
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7.0
Jun 28, 2018
06/18
by
Alexey K. Mazur
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Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it has to be invoked to account for various biological data. Using quantum chemistry, molecular mechanics, and hints from recent genetics experiments I show here that direct recognition between homologous dsDNA is possible through formation of short quadruplexes...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1510.02630
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Jun 26, 2018
06/18
by
Bartosz Rozycki; Marek Cieplak
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eye 17
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We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1502.07075
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8.0
Jun 29, 2018
06/18
by
Hemachander Subramanian; Robert A. Gatenby
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The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across all life forms. The evolutionary advantages of these broken symmetries remain unknown. Here we utilize a very simple model of hypothetical self-replicating polymers to show that asymmetric autocatalytic polymers are more successful in self-replication compared...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1605.00748
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14
Jun 27, 2018
06/18
by
A. Contini; G. Tiana
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The study of correlated mutations in alignments of homologous proteins proved to be succesful not only in the prediction of their native conformation, but also in the developement of a two-body effective potential between pairs of amino acids. In the present work we extend the effective potential, introducing a many--body term based on the same theoretical framework, making use of a principle of maximum entropy. The extended potential performs better than the two--body one in predicting the...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1506.02379
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Jun 26, 2018
06/18
by
Evan Senter; Peter Clote
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In this paper, we introduce the software suite, Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure S of a given RNA sequence has base pair distance x [resp. y] from reference structure A [resp. B], Hermes computes the exact kinetics of folding from A to B in this coarse-grained model. In particular, Hermes computes the mean first passage time from the...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1501.04648
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Jun 27, 2018
06/18
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Artem Badasyan; Yevgeni Sh. Mamasakhlisov; Rudolf Podgornik; V. Adrian Parsegian
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We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible states to the number corresponding to a helical conformation. The resulting transition phase diagram is then juxtaposed with the unusual behavior of the secondary structures in Intrinsically Disordered Proteins (IDPs) and a number of similarities are observed,...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1503.06840
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Jun 28, 2018
06/18
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Nestor Norio Oiwa; Claudette Cordeiro; Dieter W. Heermann
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The eukaryotic Cys2His2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains, responsible for gene regulation and the spatial organization of DNA. To study and understand the zinc finger DNA-protein interaction, we use the extended ladder in the DNA model proposed by Zhu, Rasmussen, Balatsky \& Bishop (2007) \cite{Zhu-2007}. Considering one single spinless electron in each nucleotide $\pi$-orbital along a double DNA chain (dDNA), we find a typical pattern for the...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1508.02913
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3.0
Jun 29, 2018
06/18
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Jacques M. Bahi; Christophe Guyeux; Antoine Perasso
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Various genome evolutionary models have been proposed these last decades to predict the evolution of a DNA sequence over time, essentially described using a mutation matrix. By essence, all of these models relate the evolution of DNA sequences to the computation of the successive powers of the mutation matrix. To make this computation possible, hypotheses are assumed for the matrix, such as symmetry and time-reversibility, which are not compatible with mutation rates that have been recently...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1608.06107
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9.0
Jun 30, 2018
06/18
by
Kelin Xia; Guo-Wei Wei
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eye 9
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Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is, for the first time, introduced for extracting molecular topological fingerprints (MTFs) based on the persistence of molecular topological invariants. MTFs are utilized for protein characterization, identification and classification. The method of slicing is...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1412.2779
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5.0
Jun 28, 2018
06/18
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Pablo Turjanski; R. Gonzalo Parra; Rocío Espada; Verónica Becher; Diego U. Ferreiro
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Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repetitions within a single repeat protein can be extremely variable at the sequence level. We propose a mathematical definition of a repeat and investigate the occurrences of these in different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1510.02469
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10.0
Jun 30, 2018
06/18
by
Ivan Dotu; Juan Antonio Garcia-Martin; Betty L. Slinger; Vinodh Mechery; Michelle M. Meyer; Peter Clote
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Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold, which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold, we design ten cis-cleaving hammerhead ribozymes, all of which are...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1408.2114
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7.0
Jun 30, 2018
06/18
by
Kelin Xia; Xin Feng; Yiying Tong; Guo Wei We
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Persistent homology is a relatively new tool often used for \emph{qualitative} analysis of intrinsic topological features in images and data originated from scientific and engineering applications. In this paper, we report novel \emph{quantitative} predictions of the energy and stability of fullerene molecules, the very first attempt in employing persistent homology in this context. The ground-state structures of a series of small fullerene molecules are first investigated with the standard...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1412.2369
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3.0
Jun 30, 2018
06/18
by
Kristopher Opron; Kelin Xia; Guo-Wei Wei
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The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions, while the protein functions, such as stability and flexibility, are solely determined by the...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1412.2786
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4.0
Jun 29, 2018
06/18
by
Karolis Uziela; Björn Wallner; Arne Elofsson
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Motivation: To assess the quality of a protein model, i.e. to estimate how close it is to its native structure, using no other information than the structure of the model has been shown to be useful for structure prediction. The state of the art method, ProQ2, is based on a machine learning approach that uses a number of features calculated from a protein model. Here, we examine if these features can be exchanged with energy terms calculated from Rosetta and if a combination of these terms can...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1602.05832
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4.0
Jun 30, 2018
06/18
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J. W. Heal; R. A. Römer; C. A. Blindauer; R. B. Freedman
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The determination of a 'folding core' can help to provide insight into the structure, flexibility, mobility and dynamics, and hence, ultimately, function of a protein - a central concern of structural biology. Changes in the folding core upon ligand binding are of particular interest because they may be relevant to drug-induced functional changes. Cyclophilin A is a multi-functional ligand-binding protein and a significant drug target. It acts principally as an enzyme during protein folding,...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1407.4436
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6.0
Jun 30, 2018
06/18
by
Nobu C. Shirai; Macoto Kikuchi
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{\alpha}-synuclein ({\alpha}-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of {\alpha}-syn is induced not only by increases in {\alpha}-syn concentration but also by macromolecular crowding. In order to investigate the coupled effect of the intrinsic disorder of {\alpha}-syn and macromolecular crowding, we construct a lattice gas model...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1411.3383
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10.0
Jun 28, 2018
06/18
by
Emilie Purvine; Kyle Monson; Elizabeth Jurrus; Keith Star; Nathan A. Baker
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There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial-time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1507.07021
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7.0
Jun 30, 2018
06/18
by
R. Capelli; C. Paissoni; P. Sormanni; G. Tiana
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The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour of large systems or to perform systematic scans of smaller systems. While powerful algorithms are available to facilitate the sampling of the conformational space, successful applications of such models are hindered by the availability of simple enough...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1402.0385
2,136
2.1K
Dec 27, 2012
12/12
by
O'Neil, Maryadele J
texts
eye 2,136
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Ill. on lining papers
Topics: Drugs, Chemicals, Biomolecules
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6.0
Jun 29, 2018
06/18
by
Duan Chen; Guowei Wei
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eye 6
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The molecular mechanism of ion channel gating and substrate modulation is elusive for many voltage gated ion channels, such as eukaryotic sodium ones. The understanding of channel functions is a pressing issue in molecular biophysics and biology. Mathematical modeling, computation and analysis of membrane channel charge transport have become an emergent field and give rise to significant contributions to our understanding of ion channel gating and function. This review summarizes recent...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1611.04573
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6.0
Jun 30, 2018
06/18
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Grzegorz Nawrocki; Marek Cieplak
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The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1405.7892
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Jun 26, 2018
06/18
by
Bartosz Rozycki; Lukasz Mioduszewski; Marek Cieplak
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eye 16
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Using coarse-grained molecular dynamics simulations, we analyze mechanically induced dissociation and unfolding of the protein complex CD48-2B4. This heterodimer is an indispensable component of the immunological system: 2B4 is a receptor on natural killer cells whereas CD48 is expressed on surfaces of various immune cells. So far, its mechanostability has not been assessed either experimentally or theoretically. We find that the dissociation processes strongly depend on the direction of...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1502.07087
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Jun 27, 2018
06/18
by
Juan Antonio Garcia-Martin; Ivan Dotu; Peter Clote
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Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure, or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1505.04210
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7.0
Jun 28, 2018
06/18
by
B. Kav; M. Ozturk; A. Kabakcioglu
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Nonlinear effects in protein dynamics are expected to play role in function, particularly of allosteric nature, by facilitating energy transfer between vibrational modes. A recently proposed method focusing on the non-Gaussian shape of the population near equilibrium projects this information onto real space in order to identify the aminoacids relevant to function. We here apply this method to three ancestral proteins in glucocorticoid receptor (GR) family and show that the mutations that...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1509.05483
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11
Jun 28, 2018
06/18
by
Jinn-Liang Liu; Bob Eisenberg
texts
eye 11
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Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi (PNPF) model for studying ion transport through biological ion channels. PNPF contains many more correlations than most models and simulations of channels, because it includes water and calculates dielectric properties consistently as outputs. This model accounts for the steric effect of ions and water molecules with different sizes and interstitial voids, the correlation effect of crowded ions with different valences,...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1506.05953
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9.0
Jun 28, 2018
06/18
by
Govardhan Reddy; D. Thirumalai
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Folding of Ubiquitin (Ub) is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained Self-Organized-Polymer model with side chains. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At $T_m$ Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at $T_m$, with multiple transitions between the...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1507.02007
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Jun 27, 2018
06/18
by
Adriana Supady; Volker Blum; Carsten Baldauf
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eye 17
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The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment of the conformation space of molecules. The algorithm is designed to work with first-principles methods, facilitated by the incorporation of local optimization and blacklisting conformers to prevent repeated evaluations of very similar solutions. The aim of...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1505.02521
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5.0
Jun 29, 2018
06/18
by
Shiyang Long; Pu Tian
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eye 5
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Protein allostery requires dynamical structural correlations. Physical origin of which, however, remain elusive despite intensive studies during last two decades. Based on analysis of molecular dynamics (MD) simulation trajectories for ten proteins with different sizes and folds, we found that nonlinear backbone torsional pair (BTP) correlations, which are spatially more long-ranged and are mainly executed by loop residues, exist extensively in most analyzed proteins. Examination of torsional...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1603.01789
