Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

Journal of Computer-Aided Molecular Design - We systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6,...     

Absence of Phase Transitions in a Class of Integer Spin Systems

We exhibit a class of integer spin systems whose free energy can be written in term of an absolutely convergent series at any temperature. This class includes spin systems on ℤ ^d interacting through infinite range pair potential polynomially decaying at large distances r at a rate 1/r ^d+ε with ε>0. It also contains the Blume-Emery-Griffiths model in the disordered phase at large values of the crystal field.     

Potts Model on Infinite Graphs and the Limit of Chromatic Polynomials

 Given an infinite graph 𝔾 quasi-transitive and amenable with maximum degree Δ, we show that reduced ground state degeneracy per site W _r (𝔾, q) of the q-state antiferromagnetic Potts model at zero temperature on 𝔾 is analytic in the variable 1/q, whenever |2Δe ³ /q|<1. This result proves, in an even stronger formulation, a conjecture originally sketched in [12] and explicitly formulated in [16 and 19], based on which a sufficient condition for W _r (𝔾, q) to be analytic at 1/q=0 is that 𝔾 is a regular lattice. Received: 16 January 2002 / Accepted: 17 October 2002 Published online: 18 February 2003 RID="*" ID="*" Partially supported by CNPq (Brazil) RID="**" ID="**" Partially supported by CNR, G.N.F.M. (Italy) Communicated by H. Spohn     

Coulomb interaction symmetries and the Mayer series in the two-dimensional dipole gas

We study the Mayer series of the two-dimensional dipole gas in the high-temperature, low-density regime. Without performing any multiscale analysis, we obtain bounds showing that the Mayer coefficients are finite in the thermodynamic limit. These bounds are obtained by exploiting a particular partial symmetry of the interaction (which we nameO-symmetry), already used in some problems related to the two-dimensional Coulomb gas. By direct bounds on some Mayer graphs we also conjecture that any technique based uniquely on theO-symmetry will not be sufficient to prove analyticity of the series.     

Reformulating the entropic contribution in molecular docking scoring functions

We have derived, in the context of the Rigid Rotor Harmonic Approximation (RRHO), a general mass and Planck's constant h independent expression for the dissociation free energy in ligand–receptor systems, featuring a systematically (anti‐binding) additive negative entropic term depending on readily available ligand–receptor quantities. The proposed RRHO expression allows to straightforwardly compute the absolute standard dissociation free energy without resorting to expensive normal mode analysis or other dynamical matrix‐based techniques for evaluating the entropic contribution, hence providing an effective scoring function for assessing docking poses with no adjustable parameters. Our RRHO formula was tested on a set of 55 ligand–receptor systems obtaining correlation coefficients and unsigned mean errors comparable to or better than those obtained with computationally demanding techniques for the dissociation entropy assessment. The proposed compact reformulation of the RRHO entropy term could constitute the basis for new and more effective scoring functions in molecular docking‐based high‐throughput virtual screening for drug discovery. © 2016 Wiley Periodicals, Inc.     

A-priori upper bounds for the set covering problem

A matrix M∈R^n×n is said to be a column sufficient matrix if the solution set of LCP(M,q) is convex for every q∈Rⁿ. In a recent article, Qin et al. (Optim. Lett. 3:265–276, 2009) studied the concept of column sufficiency property in Euclidean Jordan algebras. In this paper, we make a further study of this concept and prove numerous results relating column sufficiency with the Z and Lypaunov-like properties. We also study this property for some special linear transformations.     

Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat

The Crooks equation [Eq. (10) in J. Stat. Phys. 90, 1481 (1998)], originally derived for microscopically reversible Markovian systems, relates the work done on a system during an irreversible transformation to the free energy difference between the final and the initial state of the transformation. In the present work we provide a theoretical proof of the Crooks equation in the context of constant volume, constant temperature steered molecular dynamics simulations of systems thermostated by means of the Nosé-Hoover method (and its variant using a chain of thermostats). As a numerical test we use the folding and unfolding processes of decaalanine in vacuo at finite temperature. We show that the distribution of the irreversible work for the folding process is markedly non-Gaussian thereby implying, according to Crooks equation, that also the work distribution of the unfolding process must be inherently non-Gaussian. The clearly asymmetric behavior of the forward and backward irreversible work distributions is a signature of a non-Markovian regime for the folding/unfolding of decaalanine.     

The Mayer Series of the Lennard–Jones Gas: Improved Bounds for the Convergence Radius

We provide a lower bound for the convergence radius of the Mayer series of the Lennard–Jones gas which strongly improves on the classical bound obtained by Penrose and Ruelle 1963. To obtain this result we use an alternative estimate recently proposed by Morais et al. (J Stat Phys 2014) for a restricted class of stable and tempered pair potentials (namely those which can be written as the sum of a non-negative potential plus an absolutely integrable and stable potential) combined with a method developed by Locatelli and Schoen (J Glob Optim 22, 175–190 2002) for establishing a lower bound for the minimal interatomic distance between particles interacting via a Morse potential in a cluster of minimum-energy configurations.     

Selective photochemistry at stereogenic metal and ligand centers of cis-[Ru(diphosphine)2(H)2]: preparative, NMR, solid state, and laser flash studies

Three ruthenium complexes Λ-[cis-Ru((R,R)-Me-BPE)(2)(H)(2)] Λ-R,R-Ru1H(2), Δ-[cis-Ru((S,S)-Me-DuPHOS)(2)(H)(2)] Δ-S,S-Ru2H(2), and Λ-[cis-Ru((R,R)-Me-DuPHOS)(2)(H)(2)] Λ-R,R-Ru2H(2) (1 = (Me-BPE)(2), 2 = (Me-DuPHOS)(2)) were characterized by multinuclear NMR and CD spectroscopy in solution and by X-ray crystallography. The chiral ligands allow the full control of stereochemistry and enable mechanistic studies not otherwise available. Oxidative addition of E-H bonds (E = H, B, Si, C) was studied by steady state and laser flash photolysis in the presence of substrates. Steady state photolysis shows formation of single products with one stereoisomer. Solid state structures and circular dichroism spectra reveal a change in configuration at ruthenium for some Δ-S,S-Ru2H(2)/Λ-R,R-Ru2H(2) photoproducts from Λ to Δ (or vice versa) while the configuration for Λ-R,R-Ru1H(2) products remains unchanged as Λ. The X-ray structure of silyl hydride photoproducts suggests a residual H(1)···Si(1) interaction for Δ-[cis-Ru((R,R)-Me-DuPHOS)(2)(Et(2)SiH)(H)] and Δ-[cis-Ru((R,R)-Me-DuPHOS)(2)(PhSiH(2))(H)] but not for their Ru(R,R-BPE)(2) analogues. Molecular structures were also determined for Λ-[cis-Ru((R,R)-Me-BPE)(2)(Bpin)(H)], Λ-[Ru((S,S)-Me-DuPHOS)(2)(η(2)-C(2)H(4))], Δ-[Ru((R,R)-Me-DuPHOS)(2)(η(2)-C(2)H(4))], and trans-[Ru((R,R)-Me-DuPHOS)(2)(C(6)F(5))(H)]. In situ laser photolysis in the presence of p-H(2) generates hyperpolarized NMR spectra because of magnetically inequivalent hydrides; these experiments and low temperature photolysis with D(2) reveal that the loss of hydride ligands is concerted. The reaction intermediates [Ru(DuPHOS)(2)] and [Ru(BPE)(2)] were detected by laser flash photolysis and have spectra consistent with approximate square-planar Ru(0) structures. The rates of their reactions with H(2), D(2), HBpin, and PhSiH(3) were measured by transient kinetics. Rate constants are significantly faster for [Ru(BPE)(2)] than for [Ru(DuPHOS)(2)] and follow the substrate order H(2) > D(2) > PhSiH(3) > HBpin.