Publications of the Skolnick Research Group

Dr. Jeffrey Skolnick
Director, Center for the Study of Systems Biology

Research Interests
Computational Biology, Bioinformatics, and Systems Biology - Development of tools for the prediction of protein structure and function from sequence; functional genomics; automatic assignment of enzymes to metabolic pathways, prediction of protein tertiary and quaternary structure and folding pathways; prediction of membrane protein tertiary structure, prediction of small molecule ligands for drug discovery, prediction of druggable protein targets, drug design, equilibrium and dynamic properties of lipid bilayers; simulation of virus coat protein assembly.

Recent Submissions

  • Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations 

    Ando, Tadashi; Chow, Edmond; Saad, Yousef; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 2012-08)
    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. ...
  • GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction 

    Zhou, Hongyi; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2011-10)
    An accurate scoring function is a key component for successful protein structure prediction. To address this important unsolved problem, we develop a generalized orientation and distance-dependent all-atom statistical ...
  • 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 ...
  • 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 ...
  • 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, ...
  • 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 ...
  • 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 ...
  • Application of sparse NMR restraints to large-scale protein structure prediction 

    Li, Wei; Zhang Yang; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2004-08)
    The protein structure prediction algorithm TOUCHSTONEX that uses sparse distance restraints derived from NMR nuclear Overhauser enhancement (NOE) data to predict protein structures at low-to-medium resolution was evaluated ...
  • 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 ...
  • Onset of anthrax toxin pore formation 

    Gao, Mu; Schulten, Klaus (Georgia Institute of TechnologyBiophysical Society, 2006-05)
    Protective antigen (PA) is the anthrax toxin protein recognized by capillary morphogenesis gene 2 (CMG2), a transmembrane cellular receptor. Upon activation, seven ligand-receptor units self-assemble into a heptameric ...
  • 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 ...
  • Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper 

    Viñals, Jorge; Kolinski, Andrzej; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2002-11)
    A lattice-based 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state 

    Pokarowski, Piotr; Kolinski, Andrzej; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2003-03)
    A simple protein model restricted to the face-centered cubic lattice has been studied. The model interaction scheme includes attractive interactions between hydrophobic (H) residues, repulsive interactions between hydrophobic ...
  • 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 ...
  • 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 ...
  • 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 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 ...

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