Готові списки джерел за темами / Conformational constraint

Добірка наукової літератури з теми "Conformational constraint"

Автор: Grafiati
Опубліковано: 10 грудня 2022
Оновлено: 28 січня 2023

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Статті в журналах з теми "Conformational constraint"

1

Campeotto, F., A. Dal Palù, A. Dovier, F. Fioretto, and E. Pontelli. "A Constraint Solver for Flexible Protein Model." Journal of Artificial Intelligence Research 48 (December 30, 2013): 953–1000. http://dx.doi.org/10.1613/jair.4193.

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This paper proposes the formalization and implementation of a novel class of constraints aimed at modeling problems related to placement of multi-body systems in the 3-dimensional space. Each multi-body is a system composed of body elements, connected by joint relationships and constrained by geometric properties. The emphasis of this investigation is the use of multi-body systems to model native conformations of protein structures---where each body represents an entity of the protein (e.g., an amino acid, a small peptide) and the geometric constraints are related to the spatial properties of the composing atoms. The paper explores the use of the proposed class of constraints to support a variety of different structural analysis of proteins, such as loop modeling and structure prediction. The declarative nature of a constraint-based encoding provides elaboration tolerance and the ability to make use of any additional knowledge in the analysis studies. The filtering capabilities of the proposed constraints also allow to control the number of representative solutions that are withdrawn from the conformational space of the protein, by means of criteria driven by uniform distribution sampling principles. In this scenario it is possible to select the desired degree of precision and/or number of solutions. The filtering component automatically excludes configurations that violate the spatial and geometric properties of the composing multi-body system. The paper illustrates the implementation of a constraint solver based on the multi-body perspective and its empirical evaluation on protein structure analysis problems.
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2

ÖTVÖS, FERENC L., DMITRY S. GEMBITSKY, RICHARD F. MURPHY, and SÁNDOR LOVAS. "38 NKA, analogs with conformational constraint." Biochemical Society Transactions 26, no. 1 (February 1, 1998): S30. http://dx.doi.org/10.1042/bst026s030.

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3

Arttamangkul, Seksiri, Thomas F. Murray, Gary E. DeLander, and Jane V. Aldrich. "Synthesis and Opioid Activity of Conformationally Constrained Dynorphin A Analogs. 1. Conformational Constraint in the "Message" Sequence." Journal of Medicinal Chemistry 38, no. 13 (June 1995): 2410–17. http://dx.doi.org/10.1021/jm00013a016.

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4

Anthony, Peter C., Adelene Y. L. Sim, Vincent B. Chu, Sebastian Doniach, Steven M. Block, and Daniel Herschlag. "Electrostatics of Nucleic Acid Folding under Conformational Constraint." Journal of the American Chemical Society 134, no. 10 (February 27, 2012): 4607–14. http://dx.doi.org/10.1021/ja208466h.

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5

Capozzi, Maria Annunziata M., Claudia Pigliacelli, Giancarlo Terraneo, and Cosimo Cardellicchio. "Stacked aryl groups in P-resolved cyclic phosphonamides as a new conformational constraint." CrystEngComm 21, no. 47 (2019): 7224–32. http://dx.doi.org/10.1039/c9ce01382b.

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6

Wang, L. Y., Q. L. Deng, L. H. Lai, Y. Z. Han, and X. J. Xu. "Constraint peptide conformational analysis by Monte Carlo simulated annealing." Acta Crystallographica Section A Foundations of Crystallography 49, s1 (August 21, 1993): c152. http://dx.doi.org/10.1107/s0108767378095641.

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7

Liu, Hao-Miao, Dong Chen, Wen-Dan Xu, Li-Zhi Dang, and Hong-Bo Qin. "Total synthesis of (−)-akaol A via a conformational constraint strategy." Organic Chemistry Frontiers 5, no. 12 (2018): 1886–89. http://dx.doi.org/10.1039/c8qo00375k.

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8

Blount, Kenneth F., Fang Zhao, Thomas Hermann, and Yitzhak Tor. "Conformational Constraint as a Means for Understanding RNA-Aminoglycoside Specificity." Journal of the American Chemical Society 127, no. 27 (July 2005): 9818–29. http://dx.doi.org/10.1021/ja050918w.

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9

Fnu, Gulimirerouzi, Palak Agrawal, Gopal C. Kundu, and Georg F. Weber. "Structural Constraint of Osteopontin Facilitates Efficient Binding to CD44." Biomolecules 11, no. 6 (May 30, 2021): 813. http://dx.doi.org/10.3390/biom11060813.

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Since the original description in 1996, the interaction between the cytokine osteopontin (OPN) and the homing receptor CD44 has been extensively studied in cancer, inflammation, bone remodeling, and various other conditions. Alternative splicing and extensive posttranslational modifications by both binding partners, as well as the possibility for lateral recruitment of additional membrane receptors or soluble co-ligands into a complex have left the exact molecular requirements for high-affinity OPN-CD44 binding unresolved. We now report that there is a moderate engagement between the unmodified molecules, which results in curved double-reciprocal plots for OPN titration, suggesting the existence of two binding sites or two binding conformations. Structural constraint of OPN, by immobilization or by addition of heparin, is required for its strong ligation of CD44. Prior literature provides evidence that heparin binding to OPN prompts the unfolding of a core element in the protein. This conformational adjustment may be essential for efficient CD44 interaction. The integrin α9β1 seems to compete with the OPN-CD44 engagement, while the integrin αVβ3 reflects additive binding, suggesting that the CD44 contact sites on OPN are downstream of the RGD motif but overlap with the SVVYGLR domain. Hyaluronate has no effect, placing the relevant domain on CD44 downstream of the N-terminus.
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10

Smith, Jason G., Walther Mothes, Stephen C. Blacklow, and James M. Cunningham. "The Mature Avian Leukosis Virus Subgroup A Envelope Glycoprotein Is Metastable, and Refolding Induced by the Synergistic Effects of Receptor Binding and Low pH Is Coupled to Infection." Journal of Virology 78, no. 3 (February 1, 2004): 1403–10. http://dx.doi.org/10.1128/jvi.78.3.1403-1410.2004.

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ABSTRACT The spring-loaded model stipulates that influenza virus infection is coupled to the transition of the virus hemagglutinin (HA) from a metastable conformation to a highly stable conformation at low pH. The properties of retrovirus envelope glycoproteins indicate that infection is coupled to an analogous conformational change. As a test of this hypothesis, the requirements for avian leukosis virus A (ALV-A) infection were examined. These studies indicate that, like HA, the conformation of the mature ALV-A envelope glycoprotein is metastable and that infection is linked to refolding at low pH. However, unlike HA, low-pH activation is only observed after priming by receptor. Therefore, ALV-A infection is dependent on the synergistic effects of receptor binding and low pH, suggesting that receptor binding superimposes an additional constraint on activation of ALV-A fusion that proceeds by a mechanism comparable to that of influenza virus.
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Дисертації з теми "Conformational constraint"

1

Tucker-Kellogg, Lisa 1969. "Systematic conformational search with constraint satisfaction." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/8081.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.
Includes bibliographical references (p. 170-177).
Determining the conformations of biological molecules is a high scientific priority for biochemists and for the pharmaceutical industry. This thesis describes a systematic method for conformational search, an application of the method to determining the structure of the formyl-Met-Leu-Phe-OH (fMLF)peptide by solid-state NMR spectroscopy, and a separate project to determine the structure of a protein-DNA complex by X-ray crystallography. The purpose of the systematic search method is to enumerate all conformations of a molecule (at a given level of torsion angle resolution) that satisfy a set of local geometric constraints. Constraints would typically come from NMR experiments, but applications such as docking or homology modelling could also give rise to similar constraints. The molecule to be searched is partitioned into small subchains so that the set of possible conformations for the whole molecule may be constructed by merging the feasible conformations for the parts. However, instead of using a binary tree for straightforward divide-and-conquer, four innovations are introduced: (1) OMNIMERGE searches a subproblem for every possible subchain of the molecule. Searching every subchain provides the advantage that every possible merge is available; by choosing the most favorable merge for each subchain, the bottleneck subchain(s) and therefore the whole search may be completed more efficiently. (2) A cost function evaluates alternative divide-and-conquer trees, provided that a preliminary OMNIMERGE search of the molecule has been completed. Then dynamic programming determines the optimal partitioning or "merge-tree" for the molecule; this merge-tree can be used to improve the efficiency of future searches.
(cont.) (3) PROPAGATION shares information by enforcing arc consistency between the solution sets of overlapping subchains. By filtering the solution set of each subchain, infeasible conformations are discarded rapidly. (4) An A* function prioritizes each subchain based on estimated future costs. Subchains with sufficiently low priority can be skipped, which improves efficiency. A common theme of these four ideas is to make good choices about how to break the large search problem into lower-dimensional subproblems. These novel algorithms were implemented and the effectiveness of each is demonstrated on a well-constrained peptide with 40 degrees of freedom.
by Lisa Tucker-Kellogg.
Ph.D.
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2

Lin, Ying. "Design and synthesis of conformationally constrained glucagon analogues to study the conformational features important for glucagon bioactivity." Diss., The University of Arizona, 1993. http://hdl.handle.net/10150/186227.

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We have synthesized ten glucagon analogues that are either conformationally constrained systematically in the middle portion of the molecule, or modified from the known superagonist analogue [Lys¹⁷,¹⁸, Glu²¹]glucagon to study the structure-activity relationships of glucagon. The analogues were prepared using the solid-phase peptide synthesis method. Cyclizations were accomplished by forming the side chain lactam (amide) bridges on the resin. All peptide analogues were cleaved from the solid support, deprotected by the low-high HF procedure, and purified by a combination of gel filtration chromatography and dialysis followed by reverse-phase high performance liquid chromatography. A new characterization method for cyclic glucagon analogues using fast atom bombardment mass spectrometry with endoproteinase Asp-N peptide mapping has been developed that has provided unequivocal confirmation of the presence and site of the rings as well as the amino acid compositions. Receptor binding and adenylate cyclase activity assays and circular dichroism spectroscopy have been used to reveal the role of the structure and conformation of the middle portion of the molecule. The effects of the modification of the 17, 18 and 21 positions on the superagonist activity have also been examined. Several key features of the peptide backbone conformation responsible for binding and transduction have been further studied by theoretical calculations and computer modeling (energy minimization) using the Sybyl program.
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3

Derrer, Sam. "Medium ring lactams as peptide conformational constraints." Thesis, University of Cambridge, 1998. https://www.repository.cam.ac.uk/handle/1810/251637.

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Wacowich-Sgarbi, Shirley Ann. "Synthesis and conformational studies of constrained oligosaccharides." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0013/NQ60036.pdf.

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5

Harris, Lawrence Daniel. "Conformationally constrained amino acid analogues." Thesis, University of Oxford, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.526527.

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6

Li, Qing. "Conformationally Constrained Oligonucleotides for RNA Targeting." Doctoral thesis, Uppsala universitet, Kemisk biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-179069.

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A short oligonucleotide sequence as in a single-stranded antisense oligo nucleotides (AON) or in double-stranded small interfering RNAs (siRNA) can modulate the gene expression by targeting against the cellular mRNA, which can be potentially exploited for therapeutic purposes in the treatment of different diseases. In order to improve the efficacy of oligonucleotide-based drugs, the problem of target affinity, nuclease stability and delivery needs to be addressed. Chemical modifications of oligonucleotides have been proved to be an effective strategy to counter some of these problems. In this thesis, chemical synthesis of conformationally constrained nucleosides such as 7′-Me-carba-LNA-A, -G, -MeC and -T as well as 6′, 7′-substituted α-L-carba-LNA-T (Papers I-III) was achieved through a key free-radical cyclization. 1D and 2D NMR techniques were employed to prove the formation of bicyclic ring system by free-radical ring closure as well as to identify the specific constrained conformations in sugar moieties. These sugar-locked nucleosides were transformed to the corresponding phosphoramidites and incorporated into antisense oligonucleotides in different sequences, to evaluate their physicochemical and biochemical properties for potential antisense-based therapeutic application. AONs modified with 7′-Me-carba-LNA analogues exhibited higher RNA affinities (plus 1-4°C/modification) (Papers I & III), but AONs containing α-L-carba-LNA analogues showed decreased affinities (minus 2-3°C/ modification) (Paper II) towards complementary RNA compared to the native counterpart.  It has been demonstrated in Papers I-III that 7′-methyl substitution in α-L-carba-LNA caused the Tm drop due to a steric clash of the R-configured methyl group in the major groove of the duplex, whereas 7′-methyl group of carba-LNA locating in the minor groove of the duplex exerted no obviously negative effect on Tms, regardless of its orientation. Moreover, AONs containing 7′-Me-carba-LNA and α-L-carba-LNA derivatives were found to be nucleolytically more stable than native AONs, LNA modified AONs as well as α-L-LNA modified ones (Papers I-III). We also found in Paper II & III that the orientations of OH group in C6′ of α-L-carba-LNAs and methyl group in C7′ of 7′-Me-carba-LNAs can significantly influence the nuclease stabilities of modified AONs. It was proved that the methyl substitution in cLNAs which points towards the vicinal 3′-phosphate were more resistant to nuclease degradation than that caused by the methyl group pointing away from 3′-phosphate. Additionally, AONs modified with 7′-Me-carba-LNAs and α-L-carba-LNAs were found to elicit the RNase H mediated RNA degradation with comparable or higher rates (from 2-fold to 8-fold higher dependent upon the modification sites) as compared to the native counterpart. We also found that the cleavage patterns and rates by E. coli RNase H1 were highly dependent upon the modification sites in the AON sequences, regardless of the structural features of modifications (Papers II & III). Furthermore, we have shown that the modulations of Tms of AON/RNA duplexes are directly correlated with the aqueous solvation (Paper III).
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Reilly, Nicholas Anthony. "The synthesis of conformationally constrained peptide mimetics." Thesis, University of Liverpool, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.533934.

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8

Whitcombe, Nicole Jane. "The synthesis of conformationally constrained amino acids." Thesis, King's College London (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251584.

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9

Walke, Amol Ashok. "Synthetic approaches towards conformationally constrained amino acids." Thesis, Imperial College London, 2011. http://hdl.handle.net/10044/1/6887.

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This thesis describes research undertaken on the synthesis of conformationally constrained analogues of phenylalanine. The work is introduced by an overview of the significance of conformationally constrained amino acids in chemical biology. An example of how a potent and selective conformationally constrained tryptophan was designed and synthesized is provided. This section also reviews constrained phenylalanine analogues, detailing the influence of their constraints on their stereochemistry. The introductory Chapter ends with the description of an investigation into the use of a conformationally constrained phenylalanine analogue, Tic, in the development of potent bioactive peptides, and a discussion of the potential applications of higher homologues of Tic. The second Chapter commences with a short discussion about asymmetric synthesis and chiral resolution, followed by an example which illustrates these concepts. This is followed by a discussion on the work done in the modification and optimization of the Gibson synthesis of the amino acid Sic, which gave multigram quantities of this amino acid. Attempts to resolve racemic Sic were unsuccessful. The next Chapter begins with an introduction to aromatic C-H bond activation and a discussion of conventional Heck and oxidative Heck methodologies used in C-C bond formation. The syntheses of three novel cyclization substrates with varying degrees of electron densities in their aromatic rings are documented. Attempts to achieve intramolecular cyclization of these molecules via the Fujiwara addition method, the Gaunt oxidative Heck method and the Glorius oxidative Heck method, are described. The fourth Chapter introduces the concept of aromatic C-H bond activation via chelation assistance. A concise survey of different functional groups that are commonly used as ortho-directing groups via chelation with organometallic catalysts is presented along with an example that illustrates how this methodology has been used to synthesize potentially bioactive compounds. This is followed by a description of the synthesis of a new potential cyclization substrate with a ketone as a directing group. Attempts to achieve an intramolecular cyclization of this substrate using different [Ru] and [Rh] catalysts were unsuccessful. Chapter five begins with a brief summary of the use of gold catalysts for C-C bond formation via aromatic C-H activation. Four new substrates with potential for cyclization with varying degrees of electron densities in their aromatic rings were synthesized. Intramolecular cyclization of these substrates using Au(III) and Au(I) catalysts proved to be unsuccessful. Finally, Chapter six contains the experimental details that support the results described and discussed in Chapters 2-5.
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10

Zhao, Jielu. "Design, Syntheses and Biological Activities of Paclitaxel Analogs." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/77272.

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The conformation of paclitaxel in the bound state on the protein has been proposed to be the T-taxol conformation, and paclitaxel analogs constrained to the T-taxol conformation proved to be significantly more active than paclitaxel in both cytotoxicity and tubulin polymerization assays, thus validating the T-taxol conformation as the tubulin-binding conformation. In this work, eight compounds containing an aza-tricyclic moiety as a mimic of the baccatin core of paclitaxel have been designed and synthesized as water-soluble simplified paclitaxel analogs, among which 3.50-3.52 and 3.55 were conformationally constrained analogs designed to bind to the paclitaxel binding site of tubulin, based on their similarity to the T-taxol conformation. The open-chain analogs 3.41-3.43 and 3.57 and the bridged analogs 3.50-3.52 and 3.55 were evaluated for their antiproliferative activities against the A2780 cell lines. Analogs 3.50-3.52 and 3.55 which were designed to adopt the T-taxol conformation showed similar antiproliferative activities compared to their open-chain counterparts. They were all much less active than paclitaxel. In the second project, a series of paclitaxel analogs with various thio-containing linkers at C-2′ and C-7 positions were designed and synthesized in our lab. These analogs were attached to the surfaces of gold nanoparticles by CytImmune Sciences for the development of mutifunctional tumor-targeting agents. The native analogs and the gold bound analogs were evaluated for their antiproliferative activities against the A2780 cell line. All the compounds tested showed comparable or better activities than paclitaxel. Stability studies were performed for selected analogs in hydrolysis buffer, which showed that the analogs released paclitaxel in buffer over time. In the third project, the synthesis of a conformationally constrained paclitaxel analog which was designed to mimic the REDOR-taxol conformation was attempted. Two synthetic routes were tried and significant progress was made toward the synthesis of the conformationally constrained analog. However, both of the current synthetic routes failed to produce the key intermediate that would serve as the precursor for a ring-closing metathesis reaction to furnish the macrocyclic ring.
Ph. D.
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Книги з теми "Conformational constraint"

1

Tusa, Girolamo. Synthesis and biological activity of conformationally constrained nucleosides and nucleotides. Ottawa: National Library of Canada, 1998.

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2

Navarre, Nathalie. Design and synthesis of conformationally constrained trisaccharides for probing carbohydrate-protein interactions. Birmingham: University of Birmingham, 1999.

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3

Arttamangkul, Seksiri. Synthesis and opioid activity of conformationally constrained dynorphin A analogues. 1995.

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Частини книг з теми "Conformational constraint"

1

Gilon, Chaim, Irena Zeltser, Vered Rashti-Bahar, Dan Muller, Gal Bitan, David Halle, Giora Bar-Akiva, Zvi Selinger, and Gerardo Byk. "Backbone cyclization as a tool for imposing conformational constraint on peptides." In Peptide Chemistry 1992, 482–85. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1474-5_141.

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2

Gao, Yang, Chang-Qing Wei, Johannes Voigt, Jane Wu, Dajun Yang, and Terrence R. Burke. "Global Conformational Constraint in the Design of a Grb2 SH2 Domain Inhibitor." In Peptides: The Wave of the Future, 859–61. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0464-0_402.

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3

Liu, Ding-Guo, Yang Gao, Johannes Voigt, Jane Wu, Dajun Yang, and Terrence R. Burke. "Local Conformational Constraint in the Design of a Grb2 SH2 Domain Inhibitor." In Peptides: The Wave of the Future, 862–63. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0464-0_403.

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Ali, Fadia E., J. M. Samanen, R. Calvo, T. Romoff, T. Yellin, J. Vasko, D. Powers, et al. "Potent fibrinogen receptor antagonists bearing conformational constraints." In Peptides, 761–62. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2264-1_306.

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5

Lin, Ying, Dev Trivedi, Mara Siegel, and Victor J. Hruby. "Conformationally constrained glucagon analogs: New evidence for the conformational features important to glucagon-receptor interactions." In Peptides, 439–40. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2264-1_165.

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6

Maougal, Esma, Jean-Marc Escudier, Christophe Len, Didier Dubreuil, and Jacques Lebreton. "Synthesis of Conformationally Constrained Nucleoside Analogues." In Chemical Synthesis of Nucleoside Analogues, 345–426. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118498088.ch9.

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Kanmera, T., A. Mori, T. Minegishi, and Y. Nakao. "Conformationally constrained PTH-related protein antagonists." In Peptides 1994, 650–51. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-1468-4_297.

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Fardis, Maria, Haolun Jin, Xiaowu Chen, Manuel Tsiang, James Chen, Choung Kim, and Matthew Wright. "Conformationally Constrained Tricyclic HIV Integrase Inhibitors." In HIV-1 Integrase, 239–54. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118015377.ch16.

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Hruby, Victor J., Wieslaw Kazmierski, B. Montgomery Pettitt, and Fahad Al-Obeidi. "Conformational Constraints in the Design of Receptor Selective Peptides: Conformational Analysis and Molecular Dynamics." In Molecular Biology of Brain and Endocrine Peptidergic Systems, 13–27. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4684-8801-2_2.

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Ede, N. J., N. Lim, I. D. Rae, I. Cosic, F. M. Ng, M. I. Aguilar, and M. T. W. Hearn. "Conformationally constrained peptide analogs with hypoglycaemic activity." In Peptides, 268–70. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2264-1_95.

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Тези доповідей конференцій з теми "Conformational constraint"

1

Ming Zhang, Liqun Wang, and D. Maxwell. "Subdivision Approach to Target-Constrained Conformational Searching." In 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference. IEEE, 2005. http://dx.doi.org/10.1109/iembs.2005.1617003.

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Bowen, A. D., and Yue Shi. "Probing the Effect of Conformational Constraints on Binding." In 2012 SC Companion: High Performance Computing, Networking, Storage and Analysis (SCC). IEEE, 2012. http://dx.doi.org/10.1109/sc.companion.2012.334.

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Pohl, Radek, Lenka Poštová Slavětínská, and Dominik Rejman. "Pyrrolidine nucleotides conformationally constrained via hydrogen bonding." In XVIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2014. http://dx.doi.org/10.1135/css201414352.

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Ries, Andrew, and Shanzhong Shawn Duan. "An Emerging O(N) Model and Algorithm for Virtual Prototyping of Dynamics of Molecular Conformation." In ASME 2008 International Mechanical Engineering Congress and Exposition. ASMEDC, 2008. http://dx.doi.org/10.1115/imece2008-66985.

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Анотація:
Molecular dynamics is effective for nano-scale phenomenon analysis. There are two major computational steps associated with computer simulation of dynamics of molecular conformation and they are the calculation of the interatomic forces and the formation and solution of the equations of motion. Currently, these two computational steps are treated separately, but in this paper an O(N) (order N) procedure is presented for an integration between these computational steps. For computational costs associated with calculating the interatomic forces, an internal coordinate method (ICM) approach is used for determining potentials due to both the bonding and non-bonding interactions. Thus, the potential gradients can be expressed as a combination of the potential in absolute and relative coordinates. For computational costs associated with the formation and solution of the equations of motion for the system, a constraint method that is used in computational multibody dynamics is utilized. This frees some degrees of freedom so that Kane’s method can be applied for the recursive formation and solution of equations of motion for the atomistic molecular system. Because the inclusion of lightly excited high frequency degrees of freedom, such as inter-atomic oscillations and rotation about double bonds would force the use of very small integration step sizes, holonomic constraints are introduced to freeze these “uninteresting” degrees of freedom. By introducing these hard constraints the time scale can be appropriately sized for to provide a less computationally intensive dynamic simulation of molecular conformation. The algorithm developed improves computational speed significantly when compared with any traditional O(N3) procedure.
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Galan, M. Carmen, Andre P. Venot, John Glushka, Anne Imberty, and GeertJan Boons. "ALPHA-(2,6)-SIALYLTRANSFERASE CATALYZED SIALYLATIONS OF CONFORMATIONALLY CONSTRAINED OLIGOSACCHARIDES." In XXIst International Carbohydrate Symposium 2002. TheScientificWorld Ltd, 2002. http://dx.doi.org/10.1100/tsw.2002.455.

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LaValle, Steven M., Paul W. Finn, Lydia E. Kavraki, and Jeal-Claude Latombe. "Efficient database screening for rational drug design using pharmacophore-constrained conformational search." In the third annual international conference. New York, New York, USA: ACM Press, 1999. http://dx.doi.org/10.1145/299432.299489.

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Duan, Shanzhong, and Andrew Ries. "An Efficient O(N) Algorithm for Computer Simulation of Rigid Body Molecular Dynamics." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-42032.

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Анотація:
Molecular dynamics is effective for a nano-scale phenomenon analysis. There are two major computational costs associated with computer simulation of atomistic molecular dynamics. They are calculation of the interaction forces and formation/solution of equations of motion. In this paper, an O(N) (order N) procedure is presented for calculation of the interaction forces and formation/solution of equations of motion. For computational costs associated with potentials or interaction forces, an internal coordinate method is used. Use of the internal coordinate method makes application of multi-rigid body molecular dynamics to an atomistic molecular system become possible. The algorithm based on the method makes the calculation considerably more practical for large-scale problems encountered in molecular dynamics such as conformation dynamics of polymers. For computational costs associated with formation/solution of equations of motion, Kane method and the internal coordinate method are used for recursive formation and solution of equations of motion of an atomistic molecular system. However, in computer simulation of atomistic molecular dynamics, the inclusion of lightly excited all degrees of freedom of an atom, such as inter-atomic oscillations and rotation about double bonds with high frequencies, introduces limitations to the simulation. The high frequencies of these degrees of freedom force the use of very small integration step sizes, which severely limit the time scales for the atomic molecular simulation over long periods of time. To improve this, holonomic constraints such as strictly constant bond lengths and bond angles are introduced to freeze these high frequency degrees of freedom since they have insignificant effect on long time scale processes in conformational dynamics. In this way, the procedure developed in multibody dynamics can be utilized to achieve higher computing efficiency and an O(N) computational performance can be realized for formation/solution of equations of motion.
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Fuchi, Kazuko, Philip R. Buskohl, James J. Joo, Gregory W. Reich, and Richard A. Vaia. "Topology Optimization for Design of Origami-Based Active Mechanisms." In ASME 2014 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/detc2014-35153.

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Origami structures morph between 2D and 3D conformations along predetermined fold lines that efficiently program the form of the structure and show potential for many engineering applications. However, the enormity of the design space and the complex relationship between origami-based geometries and engineering metrics place a severe limitation on design strategies based on intuition. The presented work proposes a systematic design method using topology optimization to distribute foldline properties within a reference crease pattern, adding or removing folds through optimization, for a mechanism design. Following the work of Schenk and Guest, foldable structures are modeled as pin-joint truss structures with additional constraints on fold, or dihedral, angles. The performance of a designed origami mechanism is evaluated in 3D by applying prescribed forces and finding displacements at set locations. The integration of the concept of origami in mechanism design thus allows for the description of designs in 2D and performance in 3D. Numerical examples indicate that origami mechanisms with desired deformations can be obtained using the proposed method. A constraint on the number of foldlines is used to simplify a design.
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Eftink, Maurice R., D. Hu, and Y. W. Jia. "Fluorescence studies with conformationally constrained tryptophan analogs: implications on the mechanisms of intramolecular quenching." In OE/LASE '92, edited by Joseph R. Lakowicz. SPIE, 1992. http://dx.doi.org/10.1117/12.58198.

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Cherba, David M., William Punch, Phil Duxbury, Simon Billinge, and Pavol Juhas. "Conformation of an ideal bucky ball molecule by genetic algorithm and geometric constraint from pair distance data." In the 2005 conference. New York, New York, USA: ACM Press, 2005. http://dx.doi.org/10.1145/1068009.1068261.

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