We describe an iterative refinement procedure for computing extended precision or exact solutions to linear programming problems (LPs). Arbitrarily precise solutions can be computed by solving a sequence of closely related LPs with limited precision arithmetic. The LPs solved share the same constraint matrix as the original problem instance and are transformed only by modification of the object...

MOTIVATION Single-particle cryo electron microscopy (cryoEM) typically produces density maps of macromolecular assemblies at intermediate to low resolution (approximately 5-30 A). By fitting high-resolution structures of assembly components into these maps, pseudo-atomic models can be obtained. Optimizing the quality-of-fit of all components simultaneously is challenging due to the large search...

Vertebrate glycoprotein hormone heterodimers are stabilized by a strand of their beta-subunits known as the "seatbelt" that is wrapped around loop 2 of their alpha-subunits (alpha2). The cysteine that terminates the seatbelt is "latched" by a disulfide to a cysteine in beta-subunit loop 1 (beta1) of all vertebrate hormones except some teleost follitropins (teFSH), wherein it is latched to a cys...

An improved generalized comparative modeling method, GENECOMP, for the refinement of threading models is developed and validated on the Fischer database of 68 probe-template pairs, a standard benchmark used to evaluate threading approaches. The basic idea is to perform ab initio folding using a lattice protein model, SICHO, near the template provided by the new threading algorithm PROSPECTOR. P...

We consider a Fredholm integral equation of the second kind in L1([a, b],C), with a weakly singular kernel. Sufficient conditions are given for the existence and uniqueness of the solution. We adapt the product integration method proposed in C0([a, b],C) to apply it in L1([a, b],C), and discretize the equation. To improve the accuracy of the approximate solution, we use different iterative refi...

In first-order logic, forward search using a complete strategy such as the inverse method can get stuck deriving larger and larger consequence sets when the goal query is unprovable. This is the case even in trivial theories where backward search strategies such as tableaux methods will fail finitely. We propose a general mechanism for bounding the consequence sets by means of finite approximat...

To improve the accuracy of TASSER models especially in the limit where threading provided template alignments are of poor quality, we have developed the TASSER algorithm which uses the templates and contact restraints from TASSER generated models for iterative structure refinement. We apply TASSER to a large benchmark set of 2,773 nonhomologous single domain proteins that are 200 in length and ...

Three-dimensional models of the alpha- and beta-1 subunits of the calcium-activated potassium channel (BK) were predicted by threading modeling. A recursive approach comprising of sequence alignment and model building based on three templates was used to build these models, with the refinement of non-conserved regions carried out using threading techniques. The complex formed by the subunits wa...

Glycoprotein hormone heterodimers are stabilized by their unusual structures in which a glycosylated loop of the -subunit straddles a hole in the -subunit. This hole is formed when a cysteine at the end of a -subunit strand known as the “seatbelt” becomes “latched” by a disulfide to a cysteine in the -subunit core. The heterodimer is stabilized in part by the difficulty of threading the glycosy...