The authors describe the development and testing of a semiempirical free energy force field for use in AutoDock4 and similar grid-based docking methods. The force field is based on a comprehensive thermodynamic model that allows incorporation of intramolecular energies into the predicted free energy of binding. It also incorporates a charge-based method for evaluation of desolvation designed to...

0009-2614/$ see front matter 2008 Elsevier B.V. A doi:10.1016/j.cplett.2008.03.054 * Corresponding author. Address: Eenheid Algem Universiteit Brussel (VUB), Faculteit Wetenschappen Belgium. Fax: +32 2 629 3317. E-mail address: [email protected] (P. Jaque). We have explored the relationships between the reaction force F(n), the reaction force constant j(n) and the projected force constants of ...

A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed by electronic...

In the present work, an extensive theoretical calculation study on Histidine-Histidine dipeptide in gas phase is done by using DFT method with Gaussian 98 program. Through investigations on the molecular geometries of this molecule it is found that there is six rings in the molecules not two rings. The presence of four intramolecular hydrogen bonds is responsible for the formation of additional...

Escherichia coli single-stranded DNA (ssDNA) binding protein (SSB) is the defining bacterial member of ssDNA binding proteins essential for DNA maintenance. SSB binds ssDNA with a variable footprint of ∼30-70 nucleotides, reflecting partial or full wrapping of ssDNA around a tetramer of SSB. We directly imaged single molecules of SSB-coated ssDNA using total internal reflection fluorescence (TI...

Sister chromatid cohesion provides the mechanistic basis, together with spindle microtubules, for generating tension between bioriented chromosomes in metaphase. Pericentric chromatin forms an intramolecular loop that protrudes bidirectionally from the sister chromatid axis. The centromere lies on the surface of the chromosome at the apex of each loop. The cohesin and condensin structural maint...

The DNA is treated using the discretized wormlike bead-chain model, where each “bead” represents a 3 nm segment of relaxed DNA (1, 2). Each bead is assigned a salt-dependent charge qdna according to Stigter (3). The DNA bead-chain is also assigned an intramolecular force field comprising of stretching, bending, twisting terms that capture all aspects of DNA mechanics. The stretching energy Ustr...