Posted by: shrikantmantri | October 28, 2009

Molecular Docking Screens Using Comparative Models of Proteins.


Publication Date: 2009 Oct 21 PMID: 19845314
Authors: Fan, H. – Irwin, J. J. – Webb, B. M. – Klebe, G. – Shoichet, B. K. – Sali, A.
Journal: J Chem Inf Model

Two orders of magnitude more protein sequences can be modeled by comparative modeling than have been determined by X-ray crystallography and NMR spectroscopy. Investigators have nevertheless been cautious about using comparative models for ligand discovery because of concerns about model errors. We suggest how to exploit comparative models for molecular screens, based on docking against a wide range of crystallographic structures and comparative models with known ligands. To account for the variation in the ligand-binding pocket as it binds different ligands, we calculate “consensus” enrichment by ranking each library compound by its best docking score against all available comparative models and/or modeling templates. For the majority of the targets, the consensus enrichment for multiple models was better than or comparable to that of the holo and apo X-ray structures. Even for single models, the models are significantly more enriching than the template structure if the template is paralogous and shares more than 25% sequence identity with the target.

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Responses

  1. Picoscale modeling is exponentiating biomolecular and cytological research progress because data density can challenge the pico/femtoscale horizon of structural features that govern the quantum effects and relativistic factors controlling biomolecular states and interactions. That depends on the atomic topological function used to compute model details.
    Recent advancements in quantum science have produced the picoyoctometric, 3D, interactive video atomic model imaging function, in terms of chronons and spacons for exact, quantized, relativistic animation. This format returns clear numerical data for a full spectrum of variables. The atom’s RQT (relative quantum topological) data point imaging function is built by combination of the relativistic Einstein-Lorenz transform functions for time, mass, and energy with the workon quantized electromagnetic wave equations for frequency and wavelength.
    The atom labeled psi (Z) pulsates at the frequency {Nhu=e/h} by cycles of {e=m(c^2)} transformation of nuclear surface mass to forcons with joule values, followed by nuclear force absorption. This radiation process is limited only by spacetime boundaries of {Gravity-Time}, where gravity is the force binding space to psi, forming the GT integral atomic wavefunction. The expression is defined as the series expansion differential of nuclear output rates with quantum symmetry numbers assigned along the progression to give topology to the solutions.
    Next, the correlation function for the manifold of internal heat capacity energy particle 3D functions is extracted by rearranging the total internal momentum function to the photon gain rule and integrating it for GT limits. This produces a series of 26 topological waveparticle functions of the five classes; {+Positron, Workon, Thermon, -Electromagneton, Magnemedon}, each the 3D data image of a type of energy intermedon of the 5/2 kT J internal energy cloud, accounting for all of them.
    Those 26 energy data values intersect the sizes of the fundamental physical constants: h, h-bar, delta, nuclear magneton, beta magneton, k (series). They quantize atomic dynamics by acting as fulcrum particles. The result is the picoyoctometric, 3D, interactive video atomic model data point imaging function, responsive to keyboard input of virtual photon gain events by relativistic, quantized shifts of electron, force, and energy field states and positions.
    Images of the h-bar magnetic energy waveparticle of ~175 picoyoctometers are available online at http://www.symmecon.com with the complete RQT atomic modeling manual titled The Crystalon Door, copyright TXu1-266-788. TCD conforms to the unopposed motion of disclosure in U.S. District (NM) Court of 04/02/2001 titled The Solution to the Equation of Schrodinger.


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