Scott J. Weiner's research while affiliated with UCSF University of California, San Francisco and other places
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Publications (13)
Computational studies are used to investigate the energies of xenon binding to myoglobin and to describe pathways through the protein interior for a metmyoglobin-xenon complex. Empirical energy calculations indicate a favorable enthalpic contribution of 0.6 to 4.2 kcal/mol to xenon binding for four experimentally determined xenon sites. These calcu...
We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n−butane, dimethyl ether, methyl ethyl...
We present a combined quantum/molecular mechanical study of the trypsin-catalyzed hydrolysis of a specific tripeptide substrate, including the entire enzyme in the calculation, as well as 200 H2O molecules. The results illustrate how the enzyme and nearby H2O molecules stabilize the ionic intermediates in peptide hydrolysis, such that the reaction...
We have presented a perspective of progress in three areas of simulations of complex molecules: the development of force fields for molecular simulation; the application of computer graphics, molecular mechanics and molecular dynamics in simulations of DNA and DNA-drug complexes and the application of computer graphics, molecular mechanics and quan...
Improving the understanding of complex molecular systems is an important and interesting use of supercomputers. Computer simulation currently plays, and will continue to play, a vital role in research in this area by acting as a guide to site-specific mutagenesis. This study explains simulations of complex molecules.
We present the results of a new approach for simulating chemical reactions by using quantum mechanical and molecular mechanical methods. This approach is applied to the hydrolysis of formamide by hydroxide ion. In the gas phase, tetrahedral complex (TC) formation is calculated to proceed with no barrier and TC breakdown involves a small barrier (12...
We present the results of molecular dynamics simulations on d(C-G-C-G-A) X d(T-C-G-C-G) with fully charged phosphates with and without inclusion of counterions. The average structures found in the two simulations are similar, but the simulation with counterions does give an average helix repeat, tilt, and twist in better agreement with those found...
Molecular mechanical and ab initio (4-31G) calculations on Nα-acetyl-N-methylalaninamide have been carried out. At the molecular mechanical level, five local energy minima have been found, and the free energies have also been determined for these five structures. Addition of a dispersion energy term to the SCF quantum mechanical energies has been s...
We present the development of a force field for simulation of nucleic acids and proteins. Our approach began by obtaining equilibrium bond lengths and angles from microwave, neutron diffraction, and prior molecular mechanical calculations, torsional constants from microwave, NMR, and molecular mechanical studies, nonbonded parameters from crystal p...
Abstract: We present the development of a force field for simulation of nucleic acids and proteins. Our approach began by obtaining equilibrium bond lengths and angles from microwave, neutron diffraction, and prior molecular mechanical calculations, torsional constants from microwave, NMR, and molecular mechanical studies, nonbonded parameters from...
Citations
... The G4 nucleic acid was treated using the standard parm99 Amber force field modified with the recently developed parmbsc0 56,57 , in combination with the recently-developed corrections ε/ζOL1 and χOL4 to improve the description respectively of the ε/ζ and χ G-quadruplex torsions [58][59][60][61][62][63] . ...
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... It may be mentioned that the minima obtained by PCILO calculations were also the minima at the ab initio level for the usual amino acids, N-methylated and dehydro amino acids. In addition , the PCILO results [47] [48] for peptides containing usual [49] and unusual amino acids [50] [51] were in conformity with ab initio results [52] [53] and knowledge-based crystallographic data. [54] [55] The global, local, and low-energy minima & their combinations obtained in the φ, ψ maps and χ curves/maps in substituted diglycolides of the form Ac-{O-C * H(X)-CO} 2 -OCH 3 in identical & enantiomeric forms, have been used to generate the conformational states for substituted polyglycolides . ...
... QM calculations were performed using the B3LYP 57,58 function with 6-31G+ (d,p) basis set [59][60][61] and MM calculations were performed using the AMBER 62,63 force field equipped in Gaussian 09. The interactions between QM and MM parts were treated using mechanical embedding 64,65 . Force field for the haem group is not defined in AMBER, but even without the haem group, the cyt cb 562 scaffold was highly stable in a pilot test of MM optimization. ...
... Early FFs were limited to mostly organic molecules or specific applications. Examples are DREIDING [6] for organic and a few inorganic main group elements, and AMBER [7] or CHARMM [8] for proteins. The first universal force field, parameterized for almost the entire periodic table, was introduced with UFF [9]. ...
... z = 39.239) was selected as the grid's center. Both ligands and receptors were protonated, with the ligands receiving Gasteiger charges and the receptor receiving Kollman charges (Weiner et al., 1984). AutoDock 4.2 (The Scripps Research Institute) was used to do the molecular docking simulations that followed. ...
... 35 In this case, higher level MP2 calculations were applied to the complex of bromouracil with hypophosphite to model the X-bonding interaction to the phosphate backbone of the DNA. 66 The MP2 calculations yielded energies that accurately mirrored those of the specific geometries seen in the experimental system (Table II), indicating that the QM models were appropriate for this DNA system. ...
... As shown in Fig. 4a, the side chain of arginine in the ligand formed four hydrogen bonds with the residues D189, T190 and G219 in FLO10. The residue T190 cooperated with D189 to participate in recognizing the substrate and maintaining the negative charge of the substrate binding pocket [35]. Two hydrogen bonds were also formed between D189 Fig. 2 Analysis of the results from multiple sequence alignment. ...
... For example, Schoenborn et al. [32] explored Xe binding to sperm whale myoglobin in the 1960s. Work continued to understand the interactions more, for example the work in the 1980s by Herman and Shankar [33] and Tilton et al. [34], and has continued to today, as exemplified by the work by Turan and colleagues [31]. Work with haemoglobin has a similar history, with reports spanning back to at least the 1960s [35], work taking place in the 1980s [36], and more recent work being reported [37]. ...
... The simulation studies of the distribution of metallic counterions around the DNA double helix started from the very first research on atomistic modeling of nucleic acids [11][12][13][14][15][16][17]. The description of electrostatic interactions, in particular, the interactions with counterions, was one of the key problems that were effectively adressed by the Ewald summation technique [17,18]. ...
