Now showing items 4-23 of 73

    • Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints 

      Lee, Seung Yup; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2008-08)
      To improve tertiary structure predictions of more difficult targets, the next generation of TASSER, TASSER_2.0, has been developed. TASSER_2.0 incorporates more accurate side-chain contact restraint predictions from a new ...
    • Brownian dynamics simulation of macromolecule diffusion in a protocell 

      Ando, Tadashi; Skolnick, Jeffrey (Georgia Institute of TechnologyWorld Scientific Publishing, 2011)
      The interiors of all living cells are highly crowded with macro molecules, which differs considerably the thermodynamics and kinetics of biological reactions between in vivo and in vitro. For example, the diffusion of green ...
    • The collapse transition of semiflexible polymers. A Monte Carlo simulation of a model system 

      Kolinski, Andrzej; Skolnick, Jeffrey; Yaris, Robert (Georgia Institute of TechnologyAmerican Institute of Physics, 1986-09-15)
      Monte Carlo simulations have been performed on a diamond lattice model of semiflexible polymers for a range of flexibilities and a range of chain lengths from 50 to 800 segments. The model includes both repulsive (excluded ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • DBD-Hunter: a knowledge-based method for the prediction of DNA protein interactions 

      Gao, Mu; Skolnick, Jeffrey (Georgia Institute of TechnologyOxford University Press, 2008-05-31)
      The structures of DNA–protein complexes have illuminated the diversity of DNA–protein binding mechanisms shown by different protein families. This lack of generality could pose a great challenge for predicting DNA–protein ...
    • The dependence of all-atom statistical potentials on structural training database 

      Zhang, Chi; Liu, Song; Zhou, Hongyi; Zhou, Yaoqi (Georgia Institute of TechnologyBiophysical Society, 2004-03)
      An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high-resolution, ...
    • 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 ...
    • Development of a physics-based force field for the scoring and refinement of protein models 

      Wróblewska, Liliana; Jagielska, Anna; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2008-04)
      The minimal requirements of a physics-based potential that can refine protein structures are the existence of a correlation between the energy with native similarity and the scoring of the native structure as the lowest ...
    • Development of unified statistical potentials describing protein-protein interactions 

      Lu, Hui; Lu, Long; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2003-03)
      A residue-based and a heavy atom-based statistical pair potential are developed for use in assessing the strength of protein-protein interactions. To ensure the quality of the potentials, a nonredundant, high-quality dimer ...
    • Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides 

      Kolinski, Andrzej; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 1992-12-15)
      A discretized model of globular proteins is employed in a Monte Carlo study of the helix-coil transition of polyalanine and the collapse transition of polyvaline. The present lattice realization permits real protein crystal ...
    • Does reptation describe the dynamics of entangled, finite length polymer systems? A model simulation 

      Kolinski, Andrzej; Skolnick, Jeffrey; Yaris, Robert (Georgia Institute of TechnologyAmerican Institute of Physics, 1987-02-01)
      In order to examine the validity of the reptation model of motion in a dense collection of polymers, dynamic Monte Carlo (MC) simulations of polymer chains composed of n beads confined to a diamond lattice were undertaken ...
    • 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, ...
    • Effect of double bonds on the dynamics of hydrocarbon chains 

      Rey, Antonio; Kolinski, Andrzej; Levine, Yehudi K.; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 1992-07-15)
      Brownian dynamics simulations of isolated 18-carbon chains have been performed, both for saturated and unsaturated hydrocarbons. The effect of one or several (nonconjugated) double bonds on the properties of the chains ...
    • Effects of topological solitons on autocorrelation functions for chains of coupled torsional oscillators 

      Perchak, Dennis; Yaris, Robert; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 1983-06-01)
      Brownian dynamics computer simulations were performed on chains of coupled torsional oscillators. The purpose was to observe the changes in autocorrelation functions, related to typical experimental measurements, caused ...
    • EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference 

      Tian, Weidong; Arakaki, Adrian K.; Skolnick, Jeffrey (Georgia Institute of TechnologyOxford University Press, 2004-12-01)
      EFICAz (Enzyme Function Inference by Combined Approach) is an automatic engine for large-scale enzyme function inference that combines predictions from four different methods developed and optimized to achieve high prediction ...
    • EFICAz²: enzyme function inference by a combined approach enhanced by machine learning 

      Arakaki, Adrian K.; Huang, Ying; Skolnick, Jeffrey (Georgia Institute of TechnologyBioMed Central, 2009-04-13)
      Background: We previously developed EFICAz, an enzyme function inference approach that combines predictions from non-completely overlapping component methods. Two of the four components in the original EFICAz are based on ...