Now showing items 21-40 of 107

    • Computer simulation of the folding of coiled coils 

      Rey, Antonio; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 1994-02-01)
      A simple model capable of providing possible folding pathways of two stranded, coiled coil peptides is described and simulated using an off-lattice dynamic Monte Carlo algorithm. Short sequences of very regular repetitive ...
    • An object oriented environment for artificial evolution of protein sequences: The example of rational design of transmembrane sequences 

      Milik, Mariusz; Skolnick, Jeffrey (Georgia Institute of TechnologyMassachusetts Institute of Technology Press, 1995)
      A system is presented for generating peptide sequences with desirable properties, using combination of neural network and artificial evolution. The process is illustrated by an example of a practical problem of ...
    • Spontaneous Translocation of a Polymer across a Curved Membrane 

      Baumgärtner, Artur; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Physical Society, 1995-03-13)
      The translocation of a hydrophobic polymer across a curved bilayer membrane has been studied using Monte Carlo methods. It is found that for curved membranes the polymer crosses spontaneously and almost irreversibly from ...
    • A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations 

      Vieth, Michal; Kolinski, Andrzej; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 1995-04-15)
      A combined Monte Carlo (MC) simulation-statistical mechanical treatment is proposed to calculate the internal partition function and equilibrium constant. The method has been applied to a number of one and multidimensional ...
    • A reduced model of short range interactions in polypeptide chains 

      Kolinski, Andrzej; Milik, Mariusz; Rycombel, Jakub; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 1995-09-08)
      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 ...
    • A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes 

      Milik, Mariusz; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 1995-10)
      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 ...
    • Computer design of idealized β-motifs 

      Kolinski, Andrzej; Galazka, Wojciech; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 1995-12-15)
      A lattice model of protein conformation and dynamics is used to explore the requirements for the de novo folding from an arbitrary random coil state of idealized models of four and six-member β-barrels. A number of possible ...
    • A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants 

      Vieth, Michal; Kolinski, Andrzej; Brooks, C. L., III; Skolnick, Jeffrey (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 ...
    • Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactions 

      Kolinski, Andrzej; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 1997-07-15)
      The effect of tertiary interactions on the observed secondary structure found in the native conformation of globular proteins was examined in the context of a reduced protein model. Short-range interactions are controlled ...
    • Optimization of protein structure on lattices using a self-consistent field approach 

      Reva, Boris A.; Rykunov, D. S.; Finkelstein, Alexei V.; Skolnick, Jeffrey (Georgia Institute of TechnologyMary Ann Liebert, Inc., 1998)
      Lattice modeling of proteins is commonly used to study the protein folding problem. The reduced number of possible conformations of lattice models enormously facilitates exploration of the conformational space. In this ...
    • Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α / β proteins 

      Kolinski, Andrzej; Galazka, Wojciech; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 1998-02-08)
      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 ...
    • Computer simulations of de novo designed helical proteins 

      Sikorski, Andrzej; Kolinski, Andrzej; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 1998-07)
      In the context of reduced protein models, Monte Carlo simulations of three de novo designed helical proteins (four-member helical bundle) were performed. At low temperatures, for all proteins under consideration, protein-like ...
    • De novo simulations of the folding thermodynamics of the GCN4 leucine zipper 

      Mohanty, Debasisa; Kolinski, Andrzej; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 1999-07)
      Entropy Sampling Monte Carlo (ESMC) simulations were carried out to study the thermodynamics of the folding transition in the GCN4 leucine zipper (GCN4-lz) in the context of a reduced model. Using the calculated partition ...
    • Dynamics and Thermodynamics of β-Hairpin Assembly: Insights from Various Simulation Techniques 

      Kolinski, Andrzej; Ilkowski, Bartosz; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 1999-12)
      Small peptides that might have some features of globular proteins can provide important insights into the protein folding problem. Two simulation methods, Monte Carlo Dynamics (MCD), based on the Metropolis sampling scheme, ...
    • Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures 

      Gront, Dominik; Kolinski, Andrzej; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 2000-09-22)
      Entropy sampling Monte Carlo, the replica method, and the classical Metropolis scheme were applied in numerical studies of the collapse transition in a simple face-centered cubic lattice polymer. The force field of the ...
    • Sequence evolution and the mechanism of protein folding 

      Ortiz, Angel R.; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2000-10)
      The impact on protein evolution of the physical laws that govern folding remains obscure. Here, by analyzing in silico-evolved sequences subjected to evolutionary pressure for fast folding, it is shown that: First, a subset ...
    • Computational studies of protein folding 

      Skolnick, Jeffrey; Kolinski, Andrzej (Georgia Institute of TechnologyInstitute of Electrical and Electronics Engineers, Inc., New York, 2001-09)
      The authors describe the state of the art in the field of protein structure prediction. They also introduce Prospector, a newly developed, iterative threading algorithm for protein structure prediction that can also be ...
    • Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures 

      Zhang, Yang; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 2001-09-15)
      A new parallel-hat tempering algorithm has been developed for Monte Carlo simulations, in which a composite ensemble of noninteracting replicas of the molecule system at different temperatures is simulated, and the Markov ...
    • Simulated refolding of stretched titin immunoglobulin domains 

      Gao, Mu; Lu, Hui; Schulten, Klaus (Georgia Institute of TechnologyBiophysical Society, 2001-10)
      Steered molecular dynamics (SMD) is used to investigate forced unfolding and spontaneous refolding of immunoglobulin I27, a domain of the muscle protein titin. Previous SMD simulations revealed the events leading to ...
    • Folding rate prediction using total contact distance 

      Zhou, Hongyi; Zhou, Yaoqi (Georgia Institute of TechnologyBiophysical Society, 2002-01)
      Linear regression analysis found that either contact order (CO) or long-range order (LRO) parameter has a significant correlation with the logarithms of folding rates. This suggests that sequence separation per contact and ...