Computer simulations of protein structures and interactions

  • 282 Pages
  • 4.76 MB
  • 3734 Downloads
  • English
by
Springer-Verlag , Berlin, New York
Proteins -- Structure -- Computer simulation., Protein enginee
StatementS. Fraga, J.M.R. Parker, J.M. Pocock.
SeriesLecture notes in chemistry ;, 66
ContributionsParker, J. M. R. 1949-, Pocock, J. M. 1960-
Classifications
LC ClassificationsQP551 .F79 1995
The Physical Object
Paginationxii, 282 p. :
ID Numbers
Open LibraryOL792070M
ISBN 103540601333, 0387601333
LC Control Number95024619

Computer assisted simulations play an important role, as an auxiliary tool, in this task. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular Format: Paperback.

About this book. Lecture Notes in Chemistry Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs, vaccines, and industrial enzymes.

Computer assisted simulations play an important role, as an auxiliary tool, in this task. Computer assisted simulations play an important role, as an auxiliary tool, in this task. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics.

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Get this from a library. Computer Simulations of Protein Structures and Interactions. [S Fraga; J M R Parker; J M Pocock] -- Lecture Notes in Chemistry Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes.

The use of computer simulations in investigations of protein−protein interactions is discussed. First, crystallographic analyses of known protein−protein complexes are summarized with particular emphasis being placed on the atomic nature Computer simulations of protein structures and interactions book the interactions.

Models available for describing macromolecular association energetics are then discussed, with special reference to the treatment of Cited by: Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein–membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power.

Computer simulation of protein folding Michael Levitt* & Arieh WarsheI* Department of Chemical Physics, Weizmann Institute of Science, Rehovoth, Israel A new and Ivery simple representation of protein conforma-tions has been used together with energy minimisation and thermalisation to simulate protein folding.

Under certain. Co3+ and Ir3+ in pure liquid ammonia: Structure and dynamics from ab initio quantum mechanical charge field molecular dynamics Wahyu Dita Saputri, Salsabila Syani Sulaiman. Understanding how and why proteins take on specific shapes has long been a goal of structural biologists, but previous computer simulations were too short to fully model the process.

Abstract. The accurate modeling of protein-ligand interactions, like any prediction of macromolecular structure, requires an energy function of sufficient detail to account for all relevant interactions and a conformational search method that can reliably find the energetically favorable conformations of a heterogeneous system.

Publisher Summary The significance of the results to be obtained from the simulation of protein structures and interactions, abetted by the availability of software packages and of powerful workstations with superb graphic capabilities, is encouraging a proliferation of published : J.M.

Details Computer simulations of protein structures and interactions FB2

Garcia de la Vega, J.M.R. Parker, S. Fraga. create proteins with not only new structures but also modified and novel functions. At the core of ‘function’ lies, most generally, a physi-cal interaction between a protein and its partner: a small molecule, a substrate, a nucleic acid or another protein.

To design functional protein interactions, computational strategies have been applied to. The translocation of proteins through pores is central to many biological phenomena, such as mitochondrial protein import, protein degradation, and delivery of protein toxins to their cytosolic targets.

Because proteins typically have to pass through constrictions that are too narrow to accommodate folded structures, translocation must be coupled to protein unfolding. The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.

As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence.

To Address Problems of Simulations Minimal protein models • Capture only predominant interactions in proteins (chain connectivity ) • Allow only study of the general characteristics of folding • Review: K.A.

Dill & H.S. Chan, Nature Str. Biol. 4 () 10 Elaborated simulation techniques • Global optimization techniques. A survey of protein–protein interactions in structures derived by X‐ray crystallography of protease–inhibitor and antigen–antibody complexes shows that they form close‐packed interfaces from which water is excluded.

The interfaces are of almost constant size.

Description Computer simulations of protein structures and interactions FB2

Molecular dynamics simulations of proteins were initially developed in the early 's [1] to harness the emerging power of computers to study the motions of proteins and other biopolymers.

Molecular dynamics simulations with a wide-variety of different approximations, have been particularly successful in studying the protein folding problem, for example [2,3], and the impact of protein motions on. Computer simulations aimed at structure prediction of supersecondary motifs in proteins Article in Proteins Structure Function and Bioinformatics 45(2) December with 11 Reads.

Three-dimensional protein structure prediction methods The prediction of the 3-D structure of polypeptides based only on the amino acid sequence (primary structure) is a problem. Updated with new chapters and topics, this book provides a comprehensive description of all essential topics in contemporary pharmacokinetics and pharmacodynamics.

It also features interactive computer simulations for students to experiment and observe PK/PD models in action. Presents the essentials of pharmacokinetics and pharmacodynamics in a clear and progressive manner Helps students.

This review discusses the many roles atomistic computer simulations of macromolecular (for example, protein) receptors and their associated small-molecule ligands can play in drug discovery, including the identification of cryptic or allosteric binding sites, the enhancement of traditional virtual-screening methodologies, and the direct prediction of small-molecule binding energies.

Proteins are the most abundant substance in living cells aside from water, and their interactions with cellular functions are crucial to healthy life. When proteins fall short of their intended. Introduction to Protein Structure folding and Dynamics: What can we learn from Simulations.

The beta strand is not a stable structure (no interactions between atoms Computer simulation of protein folding, NatureMcCammon. Karplus, Dynamics of folded proteins. The Monte Carlo approach to protein/protein interaction is modeled after the well-known random sampling algorithm used in computer science.

The theory is summarized as follows: Given a sufficiently large number of initial configurations, one will either emerge as the best configuration, or eventually lead to it. Simulation of Protein Structure, Dynamics and Function in Organic Media [Valerie Daggett] on *FREE* shipping on qualifying offers.

Simulation of Protein Structure, Dynamics and Function in Organic Media. Multi-core and/or multi-threaded architectures are monopolising the market, from embedded systems to supercomputers.

However, achieving high performance with multicore is a complex task: as the number of cores per chip and/or the number of hardware threads per core continue to increase, new challenges arise in terms of scheduling, power, temperature, scalability, analysability, design. Secondary Structure refers to the coiling or folding of a polypeptide chain that gives the protein its 3-D are two types of secondary structures observed in proteins.

One type is the alpha (α) helix structure resembles a coiled spring and is secured by hydrogen bonding in the polypeptide chain. “What we’re doing is modeling those physical interactions in the computer.” Those simulations reveal the different shapes a protein’s structure can take.

What kinds of vulnerabilities are. The Interactions curriculum introduces students to science as an endeavor, a process we engage in, rather than solely a set of discoveries by others. Explore the structure of various proteins and see how the nonpolar amino acids form the core of many protein structures.

Physical models and computer simulations to help students connect.

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Molecular dynamics (MD) is a computer simulation technique that allows one to predict the time evolution of a system of interacting particles (atoms, molecules, granules). A detailed discussion of this method and the areas of its applicability can be found in several books devoted to atomistic simulation techniques, e.g., [,].receptor interaction that were developed in the past decade are reviewed in this paper.

The central two sections introduce the methods that are already established as useful tools for the qualitative and quantitative description of ligand-receptor complexes, either when the detailed atomic structure of the receptor is known or.Before a simulation can be started, an initial structure of the protein is required.

Fortunately, the structure of the B1 domain of protein G has been solved experimentally, both by x-ray crystallography and NMR. Experimentally solved protein structures are collected and distributed by the Protein .