相关论文: A Deterministic Approach to the Protein Design Pro…
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial…
Predicting three dimensional residue-residue contacts from evolutionary information in protein sequences was attempted already in the early 1990s. However, contact prediction accuracies of methods evaluated in CASP experiments before CASP11…
This paper presents efficient algorithms for solving the problem of aligning a protein structure template to a query amino-acid sequence, known as protein threading problem. We consider the problem as a special case of graph matching…
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…
We present and discuss a novel approach to the direct and inverse protein folding problem. The proposed strategy is based on a variational approach that allows the simultaneous extraction of amino acid interactions and the low-temperature…
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simplicity, captures key features of the monomer-monomer…
The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…
The aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment. Using an exactly solvable lattice model, we design…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two…
We derive an expression with four adjustable parameters that reproduces well the 20x20 Miyazawa-Jernigan potential matrix extracted from known protein structures. The numerical values of the parameters can be approximately computed from the…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes…