TL;DR: Special efforts were made to allow for appropriate display and analysis of the sets of typically 20-40 conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, and identification and listing of short distances between pairs of hydrogen atoms.

TL;DR: DL_POLY_2.0 is a general-purpose parallel molecular dynamics simulation package developed at Daresbury Laboratory and designed to run on a wide range of computers: from single processor workstations to parallel supercomputers.

TL;DR: A method (HOLE) that allows the analysis of the dimensions of the pore running through a structural model of an ion channel is presented and can be used to predict the conductance of channels using a simple empirically corrected ohmic model.

TL;DR: A set of beta-blockers with contrasted activity has been selected to test the ability of PDDs as a visualizing technique, for the identification of newbeta-blocker active compounds.

TL;DR: The most recent tools that have been developed for modeling the three-dimensional features of polysaccharides and carbohydrate polymers are presented and should allow automatic scarches for meaningful correlations between structures and functions, through exploratory data analysis.

TL;DR: This work considers molecular surfaces defined as isocontours of a function (a sum of exponential functions centered on each atom) that approximately represents electron density that can be constructed to represent the van der Waals or solvent-accessible surface of a molecular with any accuracy.

TL;DR: The face center representation of molecular surface is employed, developed by Lin et al., to investigate the complementarity of molecular interface, and it is demonstrated that in all cases, quality interface complementarity is obtained.

TL;DR: The density distributions of adsorbates at low density are well predicted by the potential maps and show that these potential profiles are relevant for other small Lennard-Jones-like molecules.

TL;DR: Similarities in the molecular structure and surface properties of the allosteric modulators of muscarinic receptors, alcuronium, gallamine, tubocurarine, and the hexamethonium compound W84, a well-known pharmacological tool, are explored by self-organizing neural networks.

TL;DR: It is shown that the activity of soybean lipoxygenase-1 is enhanced by chloride anion, phosphate, formate, borate, etc., especially at a lower concentration of substrate, which supports the hypothesis that only one, or possibly two cysteines are responsible for the loss of activity.

TL;DR: The three-dimensional interaction of the enzyme-activated (suicide) inhibitor AA 231-1 with human leukocyte elastase has been studied using computer graphics and molecular mechanics.

TL;DR: An approach to exploiting pharmacophore models is described, where structures are assembled combinatorially from user-defined fragments and flexibly overlaid into the reference frame of the pharmacophores using distance geometry and molecular mechanics.

TL;DR: The three-dimensional structure of Ulex europaeus isolectin I has been constructed using seven legume lectins for which high-resolution crystal structures were available and the predictions presented here are compared with known biochemical data.

TL;DR: It is found that small torsional changes can enhance solubility by increasing the hydrophilic accessible surface without too much affecting the values of alpha and C.

TL;DR: Local density functional calculations were employed to model isomorphous substitution of Al3+ by Na+, K+, Mg2+, Fe2+, and Fe3+ in the octahedral layer of a dioctahedral smectite clay such as montmorillonite and the results match very well with experiment.

TL;DR: The approach enables inexperienced users to confidently make full use of sophisticated modeling techniques by offering only sensible options, hiding parameter settings, and controlling program invocation and macro execution.

TL;DR: Molecular dynamics simulations of the reactions between gaseous fluorine atoms and (SiFx)n adsorbates on the Si(100) - (2 x 1) surface are performed using the SW potential and compared to simulations with the WWC reparameterized SW potential, which predicts a 2- to 3-eV lower energy threshold for reaction and a much higher reaction cross-section.

TL;DR: It is concluded that the regions of homology define functionally important segments of p40 that are fully exposed at the protein surface, and that the third domain of p 40 (and its equivalent in the cytokine receptor family) is derived from the same ancestral genes as the gastrointestinal peptides.

TL;DR: Applications are presented for 18-crown-6 and (L30)2Cu+ catenate and the "adapted STATIS" method, which should be valuable for the classification of molecular conformations and simplified visualization of MD trajectories.

TL;DR: AM1 quantum mechanical reaction coordinate (RC) calculations were run to simulate the rate-limiting deacylation (hydrolysis) reaction for a series of para-X-PhC(O)NHCH2-C(Y)-S-papain intermediates, confirming the view that the HOMOs and LUMOs should be identified, respectively, with Sthiol and N rather than the reverse, as suggested by other workers.

TL;DR: In this article, the structures and molecular properties of 95 aromatic and heteroaromatic ligands previously tested as reversible inhibitors of chymotrypsin catalysis have been calculated using AM1.

TL;DR: A desktop PC-based graphics package, UNIVIS, for visualization of three-dimensional numerical data is described, which provides for a host of other features such as extraction of various surfaces, planar cross-sections of the three- dimensional data, and property texturing.

TL;DR: A program has been written that reconstructs three-dimensional coordinates for a protein structure given a stereo C alpha diagram so that the stereo image based on the reconstructed three- dimensional coordinates optimally fits the scanned stereo image while normal C alpha stereochemistry is enforced.

TL;DR: A universal EPR simulation program has been created by the author, which shows that when D > frequency, no EPR signal can be seen from E PR simulation; when D approximately frequency, whichever X/Q/W-band is used, the EPR signals can beseen on the basis of the simulated EPR results presented.

TL;DR: A one-dimensional representation of protein structure in terms of angles between C alpha-C alpha links in a two- dimensional representation describes tertiary structure to an accuracy of approximately 3 A.

TL;DR: An approach to characterize the local contributions to hydrophobicity by using one- and two-dimensional representations of molecular channel-like cavities to compute the 3D distribution of lipophilicity in the "pore conformation" of gramicidin A.

TL;DR: By the use of the universal EPR simulation program created by the author, spin S = 3/2 and S = 5/2 systems are studied and their simulated EPR spectra at high frequencies are presented here.

TL;DR: Eadfrith was written to provide the rapid display of molecules, so that they can be interactively rotated, translated, and scaled, and then rendered in a manner suitable for photography or other high-quality output methods.