Using Correlated Parameters for Improved Ranking of Protein-Protein Docking Decoys

A successful protein-protein docking study culminates in identification of decoys at top ranks with near-native quaternary structures. However, this task remains enigmatic because no generalized scoring functions exist that effectively infer decoys according to the similarity to near-native quaternary structures. Difficulties arise because of the highly irregular nature of the protein surface and the significant variation of the nonbonding and solvation energies based on the chemical composition of the protein-protein interface. In this work, we describe a novel method combining an interface-size filter, a regression model for geometric compatibility (based on two correlated surface and packing parameters), and normalized interaction energy (calculated from correlated nonbonded and solvation energies), to effectively rank decoys from a set of 10,000 decoys. Tests on 30 unbound binary protein-protein complexes show that in 16 cases we can identify at least one decoy in top three ranks having <= 10 angstrom backbone root mean square deviation from true binding geometry. Comparisons with other state-of-art methods confirm the improved ranking power of our method without the use of any experiment-guided restraints, evolutionary information, statistical propensities, or modified interaction energy equations. Tests on 118 less-difficult bound binary protein-protein complexes with <= 35% sequence redundancy at the interface showed that in 77% cases, at least 1 in 10,000 decoys were identified with <= 5 angstrom backbone root mean square deviation from true geometry at first rank. The work will promote the use of new concepts where correlations among parameters provide more robust scoring models. It will facilitate studies involving molecular interactions, including modeling of large macromolecular assemblies and protein structure prediction. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 787-796, 2011.

Reactions of the hexachlorocyclodiphosphazane [MeNPCl3]2 with primary aromatic amines: formation of highly basic bisphosphinimines

Reactions of hexachlorocyclodiphosphazane [MeNPCl3]2 with primary aromatic amines afforded the bisphosphinimine hydrochlorides [(RNH)2(RN)PN(Me)P(NHMe)(NHR)2]+Cl- (R = Ph 1, C6H4Me-4 2 or C6H4OMe-4 3). Dehydrochlorination of 2 and 3 by methanolic KOH yielded highly basic bisphosphinimines [(RNH)2(RN)PN(Me)P(NMe)(NHR)2] (R = C6H4Me-4 4 or C6H4OMe-4 5). Compounds 1-5 have been characterised by elemental analysis and IR and NMR (H-1, C-13, P-31) spectroscopy. The structure of 2 has been confirmed by single-crystal X-ray diffraction. The short P-N bond lengths and the conformations of the PN, units can be explained on the basis of cumulative negative hyperconjugative interactions between nitrogen lone pairs and adjacent P-N sigma* orbitals. Ab initio calculations on the model phosphinimine (H2N)3P=NH and its protonated form suggest that (amino)phosphinimines would be stronger bases compared to many organic bases such as guanidine.

Robust/Optimal Temperature Profile Control of a High-Speed Aerospace Vehicle Using Neural Networks

An approximate dynamic programming (ADP)-based suboptimal neurocontroller to obtain desired temperature for a high-speed aerospace vehicle is synthesized in this paper. A I-D distributed parameter model of a fin is developed from basic thermal physics principles. "Snapshot" solutions of the dynamics are generated with a simple dynamic inversion-based feedback controller. Empirical basis functions are designed using the "proper orthogonal decomposition" (POD) technique and the snapshot solutions. A low-order nonlinear lumped parameter system to characterize the infinite dimensional system is obtained by carrying out a Galerkin projection. An ADP-based neurocontroller with a dual heuristic programming (DHP) formulation is obtained with a single-network-adaptive-critic (SNAC) controller for this approximate nonlinear model. Actual control in the original domain is calculated with the same POD basis functions through a reverse mapping. Further contribution of this paper includes development of an online robust neurocontroller to account for unmodeled dynamics and parametric uncertainties inherent in such a complex dynamic system. A neural network (NN) weight update rule that guarantees boundedness of the weights and relaxes the need for persistence of excitation (PE) condition is presented. Simulation studies show that in a fairly extensive but compact domain, any desired temperature profile can be achieved starting from any initial temperature profile. Therefore, the ADP and NN-based controllers appear to have the potential to become controller synthesis tools for nonlinear distributed parameter systems.

Thermodynamics of lectin-sugar interaction: Binding of sugars to winged bean (Psophocarpus tetragonolobus) basic agglutinin (WBAI)

Combining site of WBAI is extended and encompasses all the residues of blood group A-reactive trisaccharide [GalNAcalpha3Galbeta4Glc]. Though both of the fucose residues of A-pentasaccharide [GalNAcalpha(Fucalpha2)3Galbeta(Fucalpha3)4Glc] do not directly interact, with the combining site they thermodynamically favour the interaction of GalNAcalpha3Galbeta4Glc part of the molecule by imposing a sterically favourable orientation of the binding epitope viz. GalNAcalpha3Galbeta4Glc of the saccharide. Binding of sugars is driven by enthalpy and is devoid of heat capacity changes. This together with enthalpy-entropy compensation observed for these processes underscore the importance of water reorganization as being one of the principal determinant of protein-sugar interactions.

Capturability of realistic generalized true proportional navigation

The capturability of a realistic generalized true proportional navigation (RGTPN) guidance law, against a nonmaneuvering target, is analyzed. The RGTPN law is obtained by relaxing the somewhat unrealistic assumption of constant closing velocity, made in all earlier studies on generalized true proportional navigation (GTPN), and incorporating the actual time-varying value in the guidance law. Closed-form solutions for the complete capture region of RGTPN is obtained in terms of both zero and acceptable non-zero miss distances. It is shown that the capture region of RGTPN in the initial relative velocity space is significantly smaller than that of GTPN, for reasonable values of navigation constant (N) and angular direction (eta) of the missile commanded latax. However, for certain values of N and eta, capturability of RGTPN is found to be better. It is also shown that if in one of the versions of GTPN, which uses constant values of both the closing velocity and the line-of-sight (LOS) angular velocity in the guidance law, the corresponding realistic time-varying quantities are used, the capture region actually expands to cover the whole of the initial relative velocity space. A number of examples are given to compare the capture performance of RGTPN with other versions of the GTPN guidance laws.

Derivation and consistency of the partial functions of the ternary system involving interaction coefficients

The logarithm of activity coefficients of the components of the ternary system is derived based on the Maclaurin infinite series, which is expressed in terms of the integral property of the system and subjected to appropriate boundary conditions. The derivation of the functions involves extensive summation of various infinite series pertaining to the first-order interaction coefficients that have been shown completely to remove any truncational error. Since the conventional equations involving interaction coefficients are internally inconsistent, a consistent form of the partial functions is developed in the article using the technique just described. The thermodynamic consistency of the functions based on the Maxwell and the Gibbs-Duhem relations has been established. The derived values of the logarithmic activity coefficients of the components have been found to be in agreement with the thermodynamic data of the Fe-Cr-Ni system at 1873 K and have been found to be independent of the compositional paths.

Spatially dependent zero-frequency response functions and correlation functions in the Kondo model

We present the details of a formalism for calculating spatially varying zero-frequency response functions and equal-time correlation functions in models of magnetic and mixed-valence impurities of metals. The method is based on a combination of perturbative, thermodynamic scaling theory [H. R. Krishna-murthy and C. Jayaprakash, Phys. Rev. B 30, 2806 (1984)] and a nonperturbative technique such as the Wilson renormalization group. We illustrate the formalism for the spin-1/2 Kondo problem and present results for the conduction-spin-density�impurity-spin correlation function and conduction-electron charge density near the impurity. We also discuss qualitative features that emerge from our calculations and discuss how they can be carried over to the case of realistic models for transition-metal impurities.

Transmembrane domains participate in functions of integral membrane proteins

Integral membrane proteins have one or more transmembrane a-helical domains and carry out a variety of functions such as enzyme catalysis, transport across membranes, transducing signals as receptors of hormones and growth factors, and energy transfer in ATP synthesis. These transmembrane domains are not mere structural units anchoring the protein to the lipid bilayer but seem to-contribute in the overall activity. Recent findings in support of this are described using some typical examples-LDL receptor, growth factor receptor tyrosine kinase, HMG-CoA reductase, F-0-ATPase and adrenergic receptors. The trends in research indicate that these transmembrane domains participate in a variety of ways such as a linker, a transducer or an exchanger in the overall functions of these proteins in transfer of materials, energy and signals.

Flat connections, geometric invariants and energy of harmonic functions on compact Riemann surfaces

A geometric invariant is associated to the space of fiat connections on a G-bundle over a compact Riemann surface and is related to the energy of harmonic functions.

Performance of the generalized delta rule in structural damage detection

The paper examines the suitability of the generalized data rule in training artificial neural networks (ANN) for damage identification in structures. Several multilayer perceptron architectures are investigated for a typical bridge truss structure with simulated damage stares generated randomly. The training samples have been generated in terms of measurable structural parameters (displacements and strains) at suitable selected locations in the structure. Issues related to the performance of the network with reference to hidden layers and hidden. neurons are examined. Some heuristics are proposed for the design of neural networks for damage identification in structures. These are further supported by an investigation conducted on five other bridge truss configurations.

Some Basic Aspects of Reaction Engineering of Precipitation Processes

Analysis of precipitation reactions is extremely important in the technology of production of fine particles from the liquid phase. The control of composition and particle size in precipitation processes requires careful analysis of the several reactions that comprise the precipitation system. Since precipitation systems involve several, rapid ionic dissociation reactions among other slower ones, the faster reactions may be assumed to be nearly at equilibrium. However, the elimination of species, and the consequent reduction of the system of equations, is an aspect of analysis fraught with the possibility of subtle errors related to the violation of conservation principles. This paper shows how such errors may be avoided systematically by relying on the methods of linear algebra. Applications are demonstrated by analyzing the reactions leading to the precipitation of calcium carbonate in a stirred tank reactor as well as in a single emulsion drop. Sample calculations show that supersaturation dynamics can assume forms that can lead to subsequent dissolution of particles that have once been precipitated.

Thomas-Fermi Method For Particles Obeying Generalized Exclusion Statistics

We use the Thomas-Fermi method to examine the thermodynamics of particles obeying Haldane exclusion statistics. Specifically, we study Calogero-Sutherland particles placed in a given external potential in one dimension. For the case of a simple harmonic potential (constant density of states), we obtain the exact one-particle spatial density and a {\it closed} form for the equation of state at finite temperature, which are both new results. We then solve the problem of particles in a $x^{2/3} ~$ potential (linear density of states) and show that Bose-Einstein condensation does not occur for any statistics other than bosons.

Direct Cartesian-Space Solutions of Generalized Bloch Equations in the Rotating Frame

Analytical solutions of the generalized Bloch equations for an arbitrary set of initial values of the x, y, and z magnetization components are given in the rotating frame. The solutions involve the decoupling of the three coupled differential equations such that a third-order differential equation in each magnetization variable is obtained. In contrast to the previously reported solutions given by Torrey, the present attempt paves the way for more direct physical insight into the behavior of each magnetization component. Special cases have been discussed that highlight the utility of the general solutions. Representative trajectories of magnetization components are given, illustrating their behavior with respect to the values of off-resonance and initial conditions. (C) 1995 Academic Press, Inc.

Generation of an eight node brick element using Papcovitch-Neuber functions

Some conventional finite elements suffer from drawbacks, such as shear locking, membrane locking, etc. To overcome them researchers have developed various techniques, termed as tricks by some and variational crimes by others. Many attempts have been made, but satisfactory explanations for why some of these techniques work have not been obtained, especially in the case of solid elements. This paper attempts a simple non-conforming solid element using assumed displacement fields which satisfy the Navier equation exactly. Its behaviour under simple loadings like bending, torsion and tension is examined and comparisons are made with existing elements.

Uniform algebras generated by holomorphic and close-to-harmonic functions

The initial motivation for this paper is to discuss a more concrete approach to an approximation theorem of Axler and Shields, which says that the uniform algebra on the closed unit disc (D) over bar generated by z and h, where h is a nowhere-holomorphic harmonic function on D that is continuous up to partial derivative D, equals C((D) over bar). The abstract tools used by Axler and Shields make harmonicity of h an essential condition for their result. We use the concepts of plurisubharmonicity and polynomial convexity to show that, in fact, the same conclusion is reached if h is replaced by h + R, where R is a non-harmonic perturbation whose Laplacian is ``small'' in a certain sense.