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A combination of dynamic Monte Carlo simulation techniques with a hydropathy scale method for the prediction of the location of transmembrane fragments in membrane proteins is described. The new hydropathy scale proposed here is based on experimental data for the interactions of tripeptides with phospholipid membranes (Jacobs, R.E., White, S.H. Biochemistry(More)
We present a workflow that leverages data from chemogenomics based target predictions with Systems Biology databases to better understand off-target related toxicities. By analyzing a set of compounds that share a common toxic phenotype and by comparing the pathways they affect with pathways modulated by nontoxic compounds we are able to establish links(More)
A method for generating a full backbone protein structure from the coordinates of ␣-carbons, is presented. The method extracts information from known protein structures to generate statistical positions for the reconstructed atoms. Tests on a set of proteins structures show the algorithm to be of comparable accuracy to existing procedures. However, the(More)
Proposed is a method for locating functionally relevant atoms in protein structures and a representation of spatial arrangements of these atoms allowing for a flexible description of active sites in proteins. The search method is based on comparison of local structure features of proteins that share a common biochemical function. The method does not depend(More)
An artificial neural network system is used for pattern recognition in protein side-chain-side-chain contact maps. A back-propagation network was trained on a set of patterns which are popular in side-chain contact maps of protein structures. Several neural network architectures and different training parameters were tested to decide on the best combination(More)
A simple model of short range interactions is proposed for a reduced lattice representation of polypeptide conformation. The potential is derived on the basis of statistical regularities seen in the known crystal structures of globular proteins. This potential accounts for the generic stiffness of polypeptides, the correlation between peptide bond plates,(More)
The Monte Carlo dynamics method was used to examine the process of protein insertion into model cell membranes. The water and lipid environments were taken into account via an effective medium approximation based on coordinate-dependent hydrophobic and hydrogen bond potentials. The polypeptide chain was represented in a full-backbone atom representation as(More)
The equilibrium and dynamic properties of a new lattice model of proteins are explored in the athermal limit. In this model, consecutive a-carbons of the model polypeptide are connected by vectors of the type (+ 2, f 1,O). In all cases, the chains have a finite backbone thickness which is close to that present in real proteins. Three different polypeptides(More)
A system is presented for generating peptide sequences with desirable properties , using combination of neural network and artificial evolution. The process is illusu·ated by an example of a practical problem of generating at1ificial transbilayer pep tides. The peptides generated in the process of artificial evolution have the physico-chemical properties of(More)