Now showing items 54-73 of 73

    • 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 ...
    • Phenomenological theory of the dynamics of polymer melts. I. Analytic treatment of self-diffusion 

      Kolinski, Andrzej; Skolnick, Jeffrey; Yaris, Robert (Georgia Institute of TechnologyAmerican Institute of Physics, 1988-01-15)
      In the context of dynamic Monte Carlo (MC) simulations on dense collections of polymer chains confined to a cubic lattice, the nature of the dynamic entanglements giving rise to the degree of polymerization n, dependence ...
    • Phenomenological theory of the dynamics of polymer melts. II. Viscoelastic properties 

      Skolnick, Jeffrey; Yaris, Robert (Georgia Institute of TechnologyAmerican Institute of Physics, 1988-01-15)
      A phenomenological theory of the nonmechanical and viscoelastic properties of polymer melts is developed. Consistent with computer simulation results [A. Kolinski, J. Skolnick, and R. Yaris, J. Chem. Phys. 86, 1567, 7164, ...
    • Possible role of helix-coil transitions in the microscopic mechanism of muscle contraction 

      Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 1987-02)
      Local helix-coil transitions in the coiled coil portion of myosin have long been implicated as a possible origin of tension generation in muscle. From a statistical mechanical theory of conformational transitions in coiled ...
    • Protein structure prediction by pro-Sp3-TASSER 

      Zhou, Hongyi; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2009-03)
      An automated protein structure prediction algorithm, pro-sp3-Threading/ASSEmbly/Refinement (TASSER), is described and benchmarked. Structural templates are identified using five different scoring functions derived from the ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • Static and dynamic properties of a new lattice model of polypeptide chains 

      Kolinski, Andrzej; Milik, Mariusz; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 1991-03-01)
      The equilibrium and dynamic properties of a new lattice model of proteins are explored in the athermal limit. In this model, consecutive -carbons of the model polypeptide are connected by vectors of the type (±2,±1,0). In ...
    • Steered molecular dynamics studies of titin I1 domain unfolding 

      Gao, Mu; Wilmanns, Matthias; Schulten, Klaus (Georgia Institute of TechnologyBiophysical Society, 2002-12)
      The cardiac muscle protein titin, responsible for developing passive elasticity and extensibility of muscle, possesses about 40 immunoglobulin-like (Ig) domains in its I-band region. Atomic force microscopy (AFM) and steered ...
    • Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome 

      Zhang, Yang; DeVries, Mark E.; Skolnick, Jeffrey (Georgia Institute of TechnologyPublic Library of Science, 2006-02)
      G protein–coupled receptors (GPCRs), encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction of endogenous signal ...
    • TASSER-Lite: an automated tool for protein comparative modeling 

      Pandit, Shashi Bhushan; Zhang, Yang; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2006-12)
      This study involves the development of a rapid comparative modeling tool for homologous sequences by extension of the TASSER methodology, developed for tertiary structure prediction. This comparative modeling procedure was ...
    • TASSER_WT: A protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets 

      Lee, Seung Yup; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2010-11)
      To improve the prediction accuracy in the regime where template alignment quality is poor, an updated version of TASSER_2.0, namely TASSER_WT, was developed. TASSER_WT incorporates more accurate contact restraints from a ...
    • Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins 

      Zhang, Yang; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2004-10)
      We evaluate tertiary structure predictions on medium to large size proteins by TASSER, a new algorithm that assembles protein structures through rearranging the rigid fragments from threading templates guided by a reduced ...
    • A Threading-Based Method for the Prediction of DNABinding Proteins with Application to the Human GenomeProteins with Application to the Human Genome 

      Gao, Mu; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 2009-11-13)
      Diverse mechanisms for DNA-protein recognition have been elucidated in numerous atomic complex structures from various protein families. These structural data provide an invaluable knowledge base not only for understanding ...
    • TM-align: a protein structure alignment algorithm based on the TM-score 

      Zhang, Yang; Skolnick, Jeffrey (Georgia Institute of TechnologyOxford University Press, 2005-04-22)
      We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is ~4 times faster than CE ...
    • TOUCHSTONE II: a new approach to ab initio protein structure prediction 

      Zhang, Yang; Kolinski, Andrzej; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2003-08)
      We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting Ca atoms, with attached Cb atoms and side-chain centers of mass. The ...
    • Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model 

      Kolinski, Andrzej; Klein, Piotr; Romiszowski, Piotr; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2003-11)
      Reduced lattice models of proteins and Monte Carlo dynamics were used to simulate the initial stages of the unfolding of several proteins of various structural types, and the results were compared to experiment. The models ...