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21.
Louis Carlacci 《Journal of computer-aided molecular design》1998,12(2):195-213
[Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II bend, G-G Type II bend, and G-G Type I bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by /-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 °C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications. 相似文献
22.
Ioannis?Z.?EmirisEmail author Theodoros?G.?Nikitopoulos 《Journal of mathematical chemistry》2005,37(3):233-253
Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors 相似文献
23.
Thorsten Will Michael C. Hutter Johann Jauch Volkhard Helms 《Journal of computational chemistry》2013,34(28):2485-2492
Besides all their conformational degrees of freedom, drug‐like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection of ring‐chain tautomerism. Here, we describe an adjustable fully automatic tautomer enumeration approach, which is freely available and also incorporates the detection of ring‐chain variants. The algorithm is implemented in the MolTPC framework and accessible on SourceForge. © 2013 Wiley Periodicals, Inc. 相似文献
24.
Lukas Krep Felix Schmalz Florian Solbach Dr. Leonid Komissarov Thomas Nevolianis Dr. Wassja A. Kopp Prof. Dr. Toon Verstraelen Prof. Dr. Kai Leonhard 《Chemphyschem》2023,24(7):e202200783
In our two-paper series, we first present the development of ReaxFF CHOCl parameters using the recently published ParAMS parametrization tool. In this second part, we update the reactive Molecular Dynamics – Quantum Mechanics coupling scheme ChemTraYzer and combine it with our new ReaxFF parameters from Part I to study formation and decomposition processes of chlorinated dibenzofurans. We introduce a self-learning method for recovering failed transition-state searches that improves the overall ChemTraYzer transition-state search success rate by 10 percentage points to a total of 48 %. With ChemTraYzer, we automatically find and quantify more than 500 reactions using transition state theory and DFT. Among the discovered chlorinated dibenzofuran reactions are numerous reactions that are new to the literature. In three case studies, we discuss the set of reactions that are most relevant to the dibenzofuran literature: (i) bimolecular reactions of the chlorinated-dibenzofuran precursors phenoxy radical and 1,3,5-trichlorobenzene, (ii) dibenzofuran chlorination and pyrolysis, and (iii) oxidation of chlorinated dibenzofurans. 相似文献
25.
André Michel Gérald Villeneuve John DiMaio 《Journal of computer-aided molecular design》1991,5(6):553-569
Summary The molecular basis underlying the divergent receptor selectivity of two cyclic opioid peptides Tyr-c[N
-d-Orn2-Gly-Phe-Leu-] (c-ORN) and [d-Pen2, l-Cys5]-enkephalinamide (c-PEN) was investigated using a molecular modeling approach. Ring closure and conformational searching procedures were used to determine low-energy cyclic backbone conformers. Following reinsertion of amino acid side chains, the narcotic alkaloid 7-[(1R)-1-methyl-1-hydroxy-3-phenylpropyl]-6,14-endoethenotetrahydro oripavine (PEO) was used as a flexible template for bimolecular superpositions with each of the determined peptide ring conformers using the coplanarity and cocentricity of the phenolic rings as the minimum constraint. A vector space of PEO, accounting for all possible orientations for the C21-aromatic ring of PEO served as a geometrical locus for the aromatic ring of the Phe4 residue in the opioid peptides. Although a vast number of polypeptide conformations satisfied the criteria of the opiate pharmacophore, they could be grouped into three classes differing in magnitude and sign of the torsional angle values of the tyrosyl side chain. Only class III conformers for both c-ORN and c-PEN, having tyramine dihedral angles 1 =–150° ± 30° and 2=–155° ± 20°, had significant structural and conformational properties that were mutually compatible while respecting the PEO vector space. Comparison of these properties in the context of the divergent receptor selectivity of the studied opioid peptides suggests that the increased distortion of the peptide backbone in the closure region of c-PEN together with the pendant ,-dimethyl group, combine to generate a steric volume which is absent in c-ORN and that may be incompatible with a restrictive topography of the receptor. The nature and stereo-chemistry of substituents adjacent to the closure region of the peptides could also modulate receptor selection by interacting with a charged () or neutral () subsite. 相似文献
26.
27.
Thed0ckingpr0cedurebetweeninhibitorsandproteinisaverys0phisticatedoptimizati0npr0blem;itisverydifficuIttocarry0utminimizati0nusinggradientmeth0dssuchasthesteepestdescentmeth0d,Gauss-Newtonmethod,whichareveryeasytofallint0theI0calpotentialwellsandverydifficultt0escapefr0mthem.S0s0meheuristicmeth0dshavebeenintr0ducedint0thestudies0fmolecuIarrec0gniti0n.Howt0chooseadequate0ptin1izationmeth0dinthed0ckingprocedureiscriticaIt0thecalcuIati0nresults.Inthispaper,wedescribetheimplementati0nandc0mpari… 相似文献
28.
Summary A set of algorithms designed to enhance the display of protein binding cavities is presented. These algorithms, collectively entitled CAVITY SEARCH, allow the user to isolate and fully define the extent of a particular cavity. Solid modeling techniques are employed to produce a detailed cast of the active site region, which can then be color-coded to show electrostatic and steric interactions between the protein cavity and a bound ligand. 相似文献
29.
By extending the Levy wavefunction constrained search to Fock Space,one can define a wavefunction constrained search for electron densities in systems having noninteger number of electrons.For pure-state v-representable densities,the results are equivalent to what one would obtain with the zero-temperature grand canonical ensemble.In other cases,the wavefunction constrained search in Fock space presents an upper bound to the grand canonical ensemble functional.One advantage of the Fock-space wavefunction constrained search functional over the zero-temperature grand-canonical ensemble constrained search functional is that certain specific excited states(i.e.,those that are not ground-statev-representable) are the stationary points of the Fock-space functional.However,a potential disadvantage of the Fock-space constrained search functional is that it is not convex. 相似文献
30.
研究了广泛存在于物流作业中一类新型的装箱问题,主要特征体现在箱子使用费用是关于装载率的凹函数。为求解问题,提出了一种基于分组编码策略的改进差分进化算法,以避免常规实数和整数编码方法存在放大搜索空间的不足。针对分组编码策略,定制化设计了以促进优秀基因传播为导向的新型变异和交叉操作,另外还嵌入了以物品置换为邻域的自适应局部搜索操作以增强局部搜索能力。对以往文献给出算例在不同凹费用函数下进行测试,实验结果显示所提出的算法明显优于BFD启发式算法,并且较遗传算法也有显著性改进。 相似文献