Browsing Skolnick Research Group Publications by Title
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A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants
(Georgia Institute of TechnologyAmerican Mathematical Society, 1996)A hierarchical approach to protein folding is employed to examine the folding pathway and predict the quaternary structure of the GCN4 leucine zipper. Structures comparable in quality to experiment have been predicted. In ... 
High precision multigenome scale reannotation of enzyme function by EFICAz
(Georgia Institute of TechnologyBioMed Central, 20061213)Background: The functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to erroneous assignments. We have ... 
Identification of metabolites with anticancer properties by computational metabolomics
(Georgia Institute of TechnologyBioMed Central, 20080617)Background: Certain endogenous metabolites can influence the rate of cancer cell growth. For example, diacylglycerol, ceramides and sphingosine, NAD+ and arginine exert this effect by acting as signaling molecules, while ... 
Kinetics of conformational transitions in chain molecules
(Georgia Institute of TechnologyAmerican Institute of Physics, 19800515)A theory is developed for the rate of conformational transitions (transgauche) of bonds in chain molecules, such as alkanes and polymers. This is a multidimensional extension of Kramers' reaction rate theory. Central to ... 
The kinetics of conformational transitions: Effect of variation of bond angle bending and bond stretching force constants
(Georgia Institute of TechnologyAmerican Institute of Physics, 19811101)Conformational transitions in chain molecules have been shown to proceed via a reaction coordinate which is a localized mode involving rotations about bonds, and also bond angle bending and bond stretching. By investigating ... 
Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations
(Georgia Institute of TechnologyAmerican Institute of Physics, 201208)Hydrodynamic interactions play an important role in the dynamics of macromolecules. The most common way to take into account hydrodynamic effects in molecular simulations is in the context of a Brownian dynamics simulation. ... 
A lattice dynamics study of a Langmuir monolayer of monounsaturated fatty acids
(Georgia Institute of TechnologyAmerican Institute of Physics, 19930501)A Monte Carlo dynamics (MCD) scheme has been applied in a study of the effects of unsaturated double bonds on the internal conformational dynamics and orientational order of hydrocarbon chains arranged in a monolayer on ... 
MTASSER: an algorithm for protein quaternary structure prediction
(Georgia Institute of TechnologyBiophysical Society, 200802)In a cell, it has been estimated that each protein on average interacts with roughly 10 others, resulting in tens of thousands of proteins known or suspected to have interaction partners; of these, only a tiny fraction ... 
Mechanism and rates of conformational transitions in heterogeneous polymers
(Georgia Institute of TechnologyAmerican Institute of Physics, 19821201)A general expression is presented for the rate of a trans to gauche conformational transition of a bond in a polymer backbone. The polymer is composed of nonidentical atoms, i.e., centers of differing friction constants ... 
A minimal physically realistic proteinlike lattice model: designing an energy landscape that ensures allornone folding to a unique native state
(Georgia Institute of TechnologyBiophysical Society, 200303)A simple protein model restricted to the facecentered cubic lattice has been studied. The model interaction scheme includes attractive interactions between hydrophobic (H) residues, repulsive interactions between hydrophobic ... 
Monte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model
(Georgia Institute of TechnologyAmerican Institute of Physics, 19900915)The static and dynamic properties of a dense system of flexible lattice chain molecules, one of whose ends is constrained to lie near an impenetrable interface, have been studied by means of the dynamic Monte Carlo method. ... 
Monte Carlo dynamics of diamondlattice multichain systems
(Georgia Institute of TechnologyAmerican Institute of Physics, 19860130)We present preliminary results of Monte Carlo studies on the dynamics of multichain diamondlattice systems at considerably greater densities than those done previously. Chain dynamics were simulated by a random sequence ... 
Monte Carlo dynamics study of motions in cisunsaturated hydrocarbon chains
(Georgia Institute of TechnologyAmerican Institute of Physics, 19910901)A Monte Carlo dynamics study of the motions of hydrocarbon chains containing cis double bonds is presented. The simulations utilize the highcoordination {2 1 0} lattice for the simultaneous representation of the tetrahedrally ... 
A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes
(Georgia Institute of TechnologyBiophysical Society, 199510)A Monte Carlo Dynamics simulation was used to investigate the behavior of filamentous bacteriophage coat proteins in a model membrane environment. Our simulation agrees with the previous experimental observations that ... 
Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α / β proteins
(Georgia Institute of TechnologyAmerican Institute of Physics, 19980208)Employing a high coordination lattice model and conformational sampling based on dynamic and entropy sampling Monte Carlo protocols, computer experiments were performed on three small globular proteins, each representing ... 
Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. I. The homopolymeric melt
(Georgia Institute of TechnologyAmerican Institute of Physics, 19870615)Dynamic Monte Carlo simulations of long chains confined to a cubic lattice system at a polymer volume fraction of φ =0.5 were employed to investigate the dynamics of polymer melts. It is shown that in the range of chain ... 
Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. II. Probe polymer in a matrix of different degrees of polymerization
(Georgia Institute of TechnologyAmerican Institute of Physics, 19870615)The dynamics of a probe chain consisting of n[subscript P]=100 segments in a matrix of chains of length of n[subscript M]=50 up to nM=800 at a total volume fraction of polymer φ =0.5 have been simulated by means of cubic ... 
The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CPC Suggests an Aerobic Common Ancestor to the DeltaProteobacteria
(Georgia Institute of TechnologyInstitute of Electrical and Electronics Engineers, Inc., New York, 20080507)Anaeromyxobacter dehalogenans strain 2CPC is a versaphilic deltaProteobacterium distributed throughout many diverse soil and sediment environments. 16S rRNA gene phylogenetic analysis groups A. dehalogenans together with ... 
De novo simulations of the folding thermodynamics of the GCN4 leucine zipper
(Georgia Institute of TechnologyBiophysical Society, 199907)Entropy Sampling Monte Carlo (ESMC) simulations were carried out to study the thermodynamics of the folding transition in the GCN4 leucine zipper (GCN4lz) in the context of a reduced model. Using the calculated partition ... 
Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper
(Georgia Institute of TechnologyBiophysical Society, 200211)A latticebased model of a protein and the Monte Carlo simulation method are used to calculate the entropy loss of dimerization of the GCN4 leucine zipper. In the representation used, a protein is a sequence of interaction ...