Informatics, Modeling & Simulation – Page 70

Introduction to the Time Scale Problem

Voter A.F., Los Alamos National Laboratory, US

As motivation for the symposium on extended-scale atomistic methods, I briefly discuss the time scale problem that plagues molecular dynamics simulations, some promising recent developments for circumventing the problem, and some remaining challenges.

Extended-Scale Atomistics

Docking and Drug Discovery

Irwin J., Lorber D.M., McGovern S.L., Wei B., Shoichet B.K., Northwestern University, US

Molecular docking screens large databases of small molecules by orienting and scoring them in the binding site of a protein. Top-ranked molecules may be tested for binding affinity in vitro, and may become lead compounds, [...]

Biotechnology and Drug Discovery: Two Years Into the Third Millennium

Bussiere D., Krause K., Chiron Corporation, US

The field of drug discovery is extremely complex and ever changing, with new methodologies and technologies being introduced constantly. The following paper provides an introduction to the field as well as the cutting-edge work being [...]

Computer Aided Drug Design

Computer Program Simulation of Protein Sturcture and Theory of Mechanic Force for Protein Folding II

Lu K.U., California State University, US

In the previous paper [21], we have worked out the calculation of the coordinates of the atoms in polypeptide chain, and the mathematical procedures for computing the coordinates of atoms of the alpha helices and [...]

Competitive Template Analysis of the Fast Messy Genetic Algorithm When Applied to the Protein Structure Prediction Problem

Day R.O., Zydallis J.B., Lamont G.B., Air Force Institute of Technology, US

The Protein Structure Prediction (PSP) problem is a Grand Challenge problem among biochemists, computer scientists and engineers alike. Solving this problem involves correctly predicting the geometrical conformation of a fully folded protein. This paper focuses [...]

Solving the Protein Structure Prediction Problem Through a Multiobjective Genetic Algorithm

Day R.O., Zydallis J.B., Lamont G.B., Pachter R., Air Force Institute of Technology, US

The Protein Structure Prediction (PSP) problem is a Grand Challenge problem among biochemists, computer scientists and engineers alike. Solving this problem involves correctly predicting the geometrical conformation of a fully folded protein. This paper focuses [...]

Building and Testing Scalable Fuzzy Models of Genetic Regulation in Bacteria

Sokhansanj B.A., Rodrigue G.R., Fitch J.P., Lawrence Livermore National Laboratory, US

Recent technological advances in high-throughput data collection (reviewed in [1]) give biologists the ability to study increasingly complex systems as a whole. One example is the DNA chip or microarray, an efficient high-throughput method for [...]

Stochastic Optimization Methods for Biomolecular Structure Prediction

Herges T., Wenzel W., Institute for Nanotechnology - Karlsruhe, DE

Protein structure prediction (PSP) remains one of the main outstanding challenges of theoretical biophysical chemistry. Its goal is to predict the fully three-dimensional tertiary structure of the protein on the basis of its amino acid [...]