Дисертації з теми "Interaction energy calculation"
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Almlöf, Martin. "Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7421.
Повний текст джерелаThe ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.
For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.
A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.
A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.
The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.
Panel, Nicolas. "Étude computationnelle du domaine PDZ de Tiam1." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLX062/document.
Повний текст джерелаSmall protein domains often direct protein-protein interactions and regulate eukaryotic signalling pathways. PDZ domains are among the most widespread and best-studied. They specifically recognize the 4-10 C-terminal amino acids of target proteins. Tiam1 is a Rac GTP exchange factor that helps control cellmigration and proliferation and whose PDZ domain binds the proteins syndecan-1 (Sdc1), Caspr4, and Neurexin. Short peptides and peptidomimetics can potentially inhibit or modulate its action and act as bioreagents or therapeutics. We used computational protein design (CPD) and molecular dynamics (MD) free energy simulations to understand and engineer its peptide specificity. CPD uses a structural model and an energy function to explore the space of sequences and structures and identify stable and functional protein or peptide variants. We used our in-house Proteus CPD package to completely redesign the Tiam1 PDZ domain. The designed sequences were similar to natural PDZ domains, with similarity and fold recognition scores comarable to the widely-used Rosetta CPD package. Selected sequences, containing around 60 mutated positions out of 90, were tested by microsecond MD simulations and biophysical experiments. Four of five sequences tested experimentally (by our collaborators) displayed reversible unfolding around 50°C. Proteus also accurately scored the binding specificity of several protein and peptide variants. As a more refined model for specificity, we parameterized a semi-empirical free energy model of the Poisson-Boltzmann Linear Interaction Energy or PB/LIE form, which scores conformations extracted from explicit solvent MD simulations of PDZ:peptide complexes. With three adjustable parameters, the model accurately reproduced the experimental binding affinities of 41 variants, with a mean unsigned error of just 0.4 kcal/mol, andgave predictions for 10 new variants. The PB/LIE model was tested further by comparing to non-empirical, alchemical, MD free energy simulations, which have no adjustable parameters and were found to give chemical accuracy for 12 Tiam1:peptide complexes. The tools and insights obtained should help discover new tight binding peptides or peptidomimetics and have broad implications for engineering PDZ:peptide interactions
Ramadugu, Sai Kumar. "Carbohydrate-protein interactions: structure, dynamics and free energy calculations." Diss., University of Iowa, 2013. https://ir.uiowa.edu/etd/1731.
Повний текст джерелаChang, Zhongwen, Pär Olsson, Nils Sandberg, and Dmitry Terentyev. "Interaction Energy Calculations of Edge Dislocation with Point Defects in FCC Cu." KTH, Reaktorfysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-122396.
Повний текст джерелаQC 20130530
Generation IV reactor research and development (GENIUS)
Reid, K. S. C. "Application of interactive force and energy calculations to enzyme-substrate docking." Thesis, Imperial College London, 1987. http://hdl.handle.net/10044/1/47803.
Повний текст джерелаHermansson, Anders. "Calculating Ligand-Protein Binding Energies from Molecular Dynamics Simulations." Thesis, KTH, Skolan för kemivetenskap (CHE), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-170722.
Повний текст джерелаKumari, Vandana. "Structure-Based Computer Aided Drug Design and Analysis for Different Disease Targets." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1311612599.
Повний текст джерелаNervall, Martin. "Binding Free Energy Calculations on Ligand-Receptor Complexes Applied to Malarial Protease Inhibitors." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8338.
Повний текст джерелаVazquez, Montelongo Erik Antonio. "Computational Study of Intermolecular Interactions in Complex Chemical Systems." Thesis, University of North Texas, 2020. https://digital.library.unt.edu/ark:/67531/metadc1703283/.
Повний текст джерелаChaudhari, Mrunalkumar. "First Principles Calculations of the Site Substitution Behavior in Gamma Prime Phase in Nickel Based Superalloys." Thesis, University of North Texas, 2012. https://digital.library.unt.edu/ark:/67531/metadc149571/.
Повний текст джерелаLemkul, Justin Alan. "Molecular Modeling of the Amyloid β-Peptide: Understanding the Mechanism of Alzheimer's Disease and the Potential for Therapeutic Intervention". Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/77318.
Повний текст джерелаPh. D.
Stevenson, Paul. "Nuclear structure calculations using many-body perturbation theory with a separable interaction." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312333.
Повний текст джерелаOkazaki, S., N. Yoshii, and K. Fujimoto. "Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations." AIP Publishing, 2012. http://hdl.handle.net/2237/20840.
Повний текст джерелаVorvolakos, Angelos. "Artificial neural network methods in high energy physics and their application to the identification of quark and gluon jets in electroproton collisions." Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314217.
Повний текст джерелаCalabrò, Gaetano. "Accelerating molecular simulations : implication for rational drug design." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/16439.
Повний текст джерелаKoh, Meng hock. "Fission-barriers and energy spectra of odd-mass actinide nuclei in self-consistent mean-field calculations." Thesis, Bordeaux, 2015. http://www.theses.fr/2015BORD0208/document.
Повний текст джерелаWhile there have been numerous microscopic calculations on fission barriers of even-even compoundnuclei, there are however, relatively few such work dedicated to odd-mass nuclei. This is dueto the complications posed by the breaking of the time-reversal symmetry at the mean-field leveldue to the presence of an unpaired nucleon. In order to circumvent this difficulty, previous fission barriercalculations of odd-mass nuclei have been performed by neglecting the effect of time-reversalsymmetry breaking. This work aims to improve on the description of fission barriers as well asthe spectroscopic properties of ground and fission-isomeric state, of some odd-mass actinide nucleiby taking the effect of time-reversal symmetry breaking into account. This has been perfomedwithin a Skyrme-Hartree-Fock-plus-BCS framework with blocking, where the BCS formalism hasbeen adapted to accomodate this symmetry breaking. The Skyrme nucleon-nucleon effective forcehas been used with various sets of parameters (SIII, SkM*, SLy5*). The residual pairing interactionhas been approximated by seniority forces whose neutron and proton parameters have beenfitted to reproduce the odd-even mass differences of some actinide nuclei. The low-lying rotationalband-head energies evaluated within the Bohr-Mottelson unified model have been determined forfour well-deformed odd-nuclei (235U, 239Pu, 237Np, 241Am) yielding a good qualitative agreementto the data for odd-neutron nuclei. The agreement was significantly less good for the odd-protonnuclei, possibly due to the use of the Slater approximation for the exchange Coulomb interaction.The deformation energies of two odd-neutron nuclei (235U and 239Pu) have been calculated forsome single-particle configurations up to a point beyond the outer fission-barrier. Axial symmetrynuclear shape has been assumed while a breaking of the left-right (or intrinsic parity) symmetryhas been allowed around the outer fission-barrier. The fission-barrier heights of such odd-neutronnuclei depend significantly on the particle configurations. A special attention has been paid tothe very important rotational correction to deformation energies. In particular, the correction ofthe moment of inertia calculated from the usual Belyaev expression was considered. Overall, aqualitative agreement with available data on fission-barrier heights for the considered odd-neutronnuclei and their even neighbours has been obtained
Kedziora, Gary S. "The graphical unitary group approach to configuration interaction calculations: an application to the dipole moment and potential energy surface of the water molecule /." The Ohio State University, 1994. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487857546386283.
Повний текст джерелаBhowmick, Somnath. "Theory on lower bound energy and quantum chemical study of the interaction between lithium clusters and fluorine/fluoride." Thesis, Aix-Marseille, 2015. http://www.theses.fr/2015AIXM4394.
Повний текст джерелаIn quantum chemistry, the variational principle is widely used to calculate an upper bound to the true energy of an atomic or molecular system. Methods for calculating the lower bound value to the energy exist but are much less known. An accurate method to calculate such a lower bound would allow to provide a theoretical error bar for any quantum chemistry method. We have applied variance-like methods to calculate different lower bound energies of a hydrogen atom using Gaussian basis functions. The upper bound energy is found to be always more accurate than the lower bound energies, i.e. closer to the exact energy. The importance of singular points on mean value evaluation of quantum operators has also been brought to attention.The adsorption reactions of atomic fluorine (F) and fluoride (F$^-$) on small lithium clusters Li$_n$ (n=2-15) have been investigated using accurate quantum chemistry ab initio methods. For the smallest system, we have shown that the formation of the stable Li$_2$F and Li$_2$F$^-$ complexes proceeds via a barrierless long-range electron transfer, from the Li$_2$ to F for the neutral and conversely from F$^-$ to Li$_2$ for the anionic system. Such reactions could be fast at very low temperature. Furthermore, the formed complexes show unique long bond characteristics. For the bigger Li$_n$F/Li$_n$F$^-$ systems ($n\geqslant 4$), we have shown that the adsorption energies can be as large as 6~eV depending on the adsorption site and that more than one electronic state is implied in the adsorption process. The formed complexes show interesting "superalkali" properties and could serve as building blocks in the synthesis of charge-transfer compounds with tunable properties
Takacs, Zoltan. "Chloromethane Complexation by Cryptophanes : Host-Guest Chemistry Investigated by NMR and Quantum Chemical Calculations." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-81472.
Повний текст джерелаAt the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Accepted. Paper 5: Manuscript.
Poudel, Pramod Prasad. "NOVEL AROMATIC ION–PAIRS: SYNERGY BETWEEN ELECTROSTATICS AND Π-FACE AROMATIC INTERACTIONS". UKnowledge, 2012. http://uknowledge.uky.edu/chemistry_etds/4.
Повний текст джерелаJämbeck, Joakim P. M. "Computer Simulations of Heterogenous Biomembranes." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-101297.
Повний текст джерелаDaggag, Dalia. "Computational Study on Binding of Naturally Occurring Aromatic and Cyclic Amino Acids with Graphene." DigitalCommons@Robert W. Woodruff Library, Atlanta University Center, 2019. http://digitalcommons.auctr.edu/cauetds/203.
Повний текст джерелаBuch, Mundó Ignasi 1984. "Investigation of protein-ligand interactions using high-throughput all-atom molecular dynamics simulations." Doctoral thesis, Universitat Pompeu Fabra, 2012. http://hdl.handle.net/10803/101407.
Повний текст джерелаDelandar, Arash Hosseinzadeh. "Modeling defect structure evolution in spent nuclear fuel container materials." Doctoral thesis, KTH, Materialteknologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-206175.
Повний текст джерелаQC 20170428
Roux, Raphaël. "Étude probabiliste de systèmes de particules en interaction : applications à la simulation moléculaire." Phd thesis, Université Paris-Est, 2010. http://tel.archives-ouvertes.fr/tel-00597479.
Повний текст джерелаRemmert, Sarah M. "Reduced dimensionality quantum dynamics of chemical reactions." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:7f96405f-105c-4ca3-9b8a-06f77d84606a.
Повний текст джерелаZhang, Jiajing. "Insight into biomolecular structure, interaction and energetics from modeling and simulation." 2011. http://hdl.handle.net/2152/20672.
Повний текст джерелаtext
Chen, Shih-Yuan, and 陳仕元. "Molecular Dynamics Study and Binding Free Energy Calculation on Recognition and Interaction Between Antibiotics and Oligonucleotides: (I) Mithramycin and DNA (II) Aminoglycosides and Ribosomal RNA A-Site." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/87189327231034454761.
Повний текст джерела國立清華大學
分子醫學研究所
98
Molecular dynamics (MD) simulations allow detail analysis of structural dynamics of atomic–level phenomena such as binding recognition fundamental in Biology field. Binding interaction involved between (bio) –molecules can be evaluated by binding free energy calculation base on the law of thermodynamics. Conformational flexibility essential for investigating dynamic property can be estimated by calculating conformational entropy such as principal components analysis. Combination with these techniques can provide reasonable explanations for atomic–level phenomena that are difficult to explain on the basis of static models alone. Here we present the results of a series of conventional MD simulations on recognition and interaction between (I) a mithramycin dimer and a DNA duplex, (II) several aminoglycoside antibiotics and an oligonucleotide corresponding to rRNA A–site. Both kinds of antibiotics consist of a core structure where several sugar ring substitutions at different carbon positions. In part I of the study, we successfully built the dynamics model corresponding to the experimental structure and binding affinity, discussed the binding interaction, and found the cooperativity between this GC–specific DNA binding antibiotic and a decanucleotide duplex of two GC binding sites to be in an anticooperative manner. Following the MD protocol and modification of the force field parameters for this sugar–linked antibiotic, in part II of the study, we compared the binding recognition and hydration patterns between several aminoglycoside antibiotics and a RNA duplex corresponding to the aminoacyl–tRNA decoding site (A–site) of the 16S rRNA on the 30S subunit which is a crucial component of the bacterial translational machinery. We have built several dynamic models with reasonable binding free energies showing good linear correlation with the experimental data. The hydration sites around the U1406·U1495 pair in the A–site were analyzed to distinguish tightly bound water molecules from fast–exchanging ones which has been suggested to be useful for rational drug design. We found that the hydration sites with long residence time identified between ring III of two 4,6–disubstituted antibiotics (tobramycin and kanamycin A) and phosphate oxygen atoms of G1405/U1406 may be worthy of further exploration for rational design of this kind.
Yang, Tianyi. "Free energy calculations of biopolymeric systems at cellular interface." 2009. http://hdl.handle.net/2152/7477.
Повний текст джерелаtext
Xu, Fang. "Resonance-energy-transfer-based fluorescence imaging and free energy perturbation calculation." Thesis, 2018. https://doi.org/10.7916/D8PP0HKZ.
Повний текст джерелаRobin, Abel. "Trajectory and channeling effects in the scattering of ions off a metal surface - Probing the electronic density corrugation at a surface by grazing axial ion channeling." Doctoral thesis, 2003. https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-2003112519.
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