22 p. ; 23 cm
Topic: Biomolecules
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2.0
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Topics: Biochemistry, Biomolecules, Biomolecules -- Structure, Biophysics
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web
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Biomolecules dumped with WikiTeam tools.
Topics: wiki, wikiteam, wikispaces, Biomolecules, biomolecules, biomolecules.wikispaces.com
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0.0
texts
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x, 176 p. : 28 cm
Topics: Biomolecules -- Analysis -- Congresses, Biomolecules -- Spectra -- Congresses
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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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x, 646 p. : 25 cm
Topics: Biomolecules -- Spectra -- Congresses, Biomolecules -- Analysis -- 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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3.0
texts
eye 3
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vii, 146 p. : 28 cm
Topics: Biomolecules -- Analysis -- Congresses, Biomolecules -- Spectra -- Congresses
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20
May 9, 2020
05/20
by
Schlick, Tamar
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eye 20
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xliii, 634 p. : 25 cm
Topics: Biomolecules -- Models, Biomolecules -- Models -- Computer simulation
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5.0
May 2, 2022
05/22
by
Dechow, Frederick J
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eye 5
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x, 490 p. : 25 cm
Topics: Biomolecules -- Separation, Biomolecules -- Purification, Biotechnology -- Technique
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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
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Aug 19, 2015
08/15
by
Collins, W. P
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Includes bibliographies and index
Topics: Immunoassay, Biomolecules
Click here to view the University of Florida catalog record
Topics: Nanoparticles, Biomolecules
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4.0
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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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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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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5.0
Apr 28, 2021
04/21
by
International Symposium on Biomolecular Structure, Conformation, Function, and Evolution (1978 : Madras, India)
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2 v. : 26 cm
Topic: Biomolecules -- Congresses
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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 29, 2018
06/18
by
Bartosz Rozycki; Marek Cieplak
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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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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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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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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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5.0
Jun 30, 2018
06/18
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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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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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3.0
Jun 30, 2018
06/18
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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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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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3.0
Jun 29, 2018
06/18
by
Marie Doumic; Sarah Eugene; Philippe Robert
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Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated experiments.To analyse the stochastic nature of this phenomenon, one of the simplest models considers two populations of chemical components: monomers and polymerised monomers. Initially there are only monomers. There are two reactions for the polymerization of a...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1603.06335
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5.0
Jun 29, 2018
06/18
by
Karolis Uziela; David Menéndez Hurtado; Björn Wallner; Arne Elofsson
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Summary: Protein quality assessment is a long-standing problem in bioinformatics. For more than a decade we have developed state-of-art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation has increased from 0.60 in ProQ to 0.81 in ProQ2 and 0.85 in ProQ3 mainly by adding a large set of carefully tuned descriptions of a protein. Here, we show that a substantial improvement can be obtained using exactly the same inputs as in ProQ2 or ProQ3 but...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1610.05189
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4.0
Jun 30, 2018
06/18
by
Grzegorz Nawrocki; Marek Cieplak
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We calculate potentials of the mean force for twenty amino acids in the vicinity of the (111) surface of gold, for several dipeptides, and for some analogs of the side chains, using molecular dynamics simulations and the umbrella sampling method. We compare results obtained within three different force fields: one hydrophobic (for a contaminated surface) and two hydrophilic. All of these fields lead to good binding with very different specificities and different patterns in the density and...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1405.7926
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5.0
Jun 30, 2018
06/18
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Liang Ding; Xingran Xue; Sal LaMarca; Mohammad Mohebbi; Abdul Samad; Russell L. Malmberg; Liming Cai
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Given the importance of non-coding RNAs to cellular regulatory functions and rapid growth of RNA transcripts, computational prediction of RNA tertiary structure remains highly demanded yet significantly challenging. Even for a short RNA sequence, the space of tertiary conformations is immense; existing methods to identify native-like conformations mostly resort to random sampling of conformations to gain computational feasibility. However native conformations may not be examined and prediction...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1407.7080
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Jun 27, 2018
06/18
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Monique M. Tirion
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Protein data bank entries obtain distinct, reproducible flexibility characteristics determined by normal mode analyses of their three dimensional coordinate files. We study the effectiveness and sensitivity of this technique by analyzing the results on one class of glycosidases: family 10 xylanases. A conserved tryptophan that appears to affect access to the active site can be in one of two conformations according to X-ray crystallographic electron density data. The two alternate orientations...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1504.07303
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6.0
Jun 29, 2018
06/18
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Cameron Mura
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Sm proteins were discovered nearly 20 years ago as a group of small antigenic proteins ($\approx$ 90-120 residues). Since then, an extensive amount of biochemical and genetic data have illuminated the crucial roles of these proteins in forming ribonucleoprotein (RNP) complexes that are used in RNA processing, e.g., spliceosomal removal of introns from pre-mRNAs. Spliceosomes are large macromolecular machines that are comparable to ribosomes in size and complexity, and are composed of...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1606.03630
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6.0
Jun 30, 2018
06/18
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Tristan Cragnolini; Yoann Laurin; Philippe Derreumaux; Samuela Pasquali
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HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show that non-canonical and multiple base interactions are necessary to capture the full physical behavior of complex RNAs. In this paper we give a full account of the model and we present results on the folding, stability and free energy surfaces of 16 systems with...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1404.0568
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28
Jun 28, 2018
06/18
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Ryan M. Harrison; Flavio Romano; Thomas E. Ouldridge; Ard A. Louis; Jonathan P. K. Doye
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DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of these studies, however, remain controversial. We use a coarse-grained model, previously fitted to DNA's basic thermodynamic and mechanical properties, to explore strongly bent systems. We find that as the end-to-end distance is decreased sufficiently short...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1506.09005
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7.0
Jun 30, 2018
06/18
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Rocío Espada; R. Gonzalo Parra; Thierry Mora; Aleksandra M. Walczak; Diego U. Ferreiro
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Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing covariations in extant sequences. Still, many natural proteins that fold into the same structural topology show different stabilization energies, and these are often related to their physiological behavior. We propose a description for the energetic variation given...
Topics: Quantitative Biology, Biomolecules
Source: http://arxiv.org/abs/1703.03449
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3.0
Jun 30, 2018
06/18
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W. Wendell Smith; Po-Yi Ho; Corey S. O'Hern
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We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of single-molecule fluorescence resonance energy transfer data on the inter-residue separations for 36 pairs...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1407.0447
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4.0
Jun 30, 2018
06/18
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J. W. Heal; S. A. Wells; R. B. Freedman; R. A. Römer
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Determining the folding core of a protein yields information about its folding process and dynamics. The experimental procedures for identifying the amino acids which make up the folding core include hydrogen-deuterium exchange and $\Phi$-value analysis and can be expensive and time consuming. As such there is a desire to improve upon existing methods for determining protein folding cores theoretically. Here, we use a combined method of rigidity analysis alongside coarse-grained simulations of...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1407.4440
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15
Jun 27, 2018
06/18
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S. V. Kozyrev
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eye 15
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We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids, conformation), averaged over some balls in the spaces of sequences and conformations. These frequencies can be estimated due to smallness of epsilon-entropy of the set of conformations of protein fragments. We consider statistical potentials for protein fragments...
Topics: Biomolecules, Quantitative Biology
Source: http://arxiv.org/abs/1504.03940
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4.0
Jun 29, 2018
06/18
by
Karolis Uziela; Björn Wallner; Arne Elofsson
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eye 4
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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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3.0
Jun 30, 2018
06/18
by
Kristopher Opron; Kelin Xia; Guo-Wei Wei
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eye 3
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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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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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7.0
Jun 30, 2018
06/18
by
Kelin Xia; Xin Feng; Yiying Tong; Guo Wei We
texts
eye 7
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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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9.0
Jun 30, 2018
06/18
by
Kelin Xia; Guo-Wei Wei
texts
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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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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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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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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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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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6.0
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
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Jun 26, 2018
06/18
by
Evan Senter; Peter Clote
texts
eye 16
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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
