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- Garrett M. Morris, David S. Goodsell, +4 authors Arthur J. Olson
- Journal of Computational Chemistry
- 1998

A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a Lamarckian model of genetics, in which environmental adaptations of… (More)

Evolutionary algorithms have been successfully applied to a variety of molecular structure prediction problems. In this paper we reconsider the design of genetic algorithms that have been applied to a simple protein structure prediction problem. Our analysis considers the impact of several algorithmic factors for this problem: the conformational… (More)

- Avi Ostfeld, James G. Uber, +31 authors Tom Walski
- 2008

Following the events of September 11, 2001, in the United States, world public awareness for possible terrorist attacks on water supply systems has increased dramatically. Among the different threats for a water distribution system, the most difficult to address is a deliberate chemical or biological contaminant injection, due to both the uncertainty of the… (More)

- William E. Hart, Michael H. Goldbaum, Brad Côté, Paul Kube, Mark R. Nelson
- I. J. Medical Informatics
- 1999

Automatic measurement of blood vessel tortuosity is a useful capability for automatic ophthalmological diagnostic tools. We describe a suite of automated tortuosity measures for blood vessel segments extracted from RGB retinal images. The tortuosity measures were evaluated in two classification tasks: (1) classifying the tortuosity of blood vessel segments… (More)

We present a mixed-integer programming (MIP) formulation for sensor placement optimization in municipal water distribution systems that includes the temporal characteristics of contamination events and their impacts. Typical network water quality simulations track contaminant concentration and movement over time, computing contaminant concentration… (More)

We present a model for optimizing the placement of sensors in municipal water networks to detect maliciously-injected contaminants. An optimal sensor configuration minimizes the expected fraction of the population at risk. We formulate this problem as an integer program, which can be solved with generally available IP solvers. We find optimal sensor… (More)

- William E. Hart, Sorin Istrail
- STOC
- 1995

We present performance-guaranteed approximation algorithms for the protein folding problem in the hydrophobichydrophilic model, Dill (1985). To our knowledge, our algorithms arethe first approximation algorithms inthe literature with guaranteed performance for this model, Dill (1994). The hydrophobic-hydrophilic model abstracts the dominant force of protein… (More)

- William E. Hart, Sorin Istrail
- Journal of Computational Biology
- 1996

We present performance-guaranteed approximation algorithms for the protein folding problem in the hydrophobic-hydrophilic model (Dill, 1985). Our algorithms are the first approximation algorithms in the literature with guaranteed performance for this model (Dill, 1994). The hydrophobic-hydrophilic model abstracts the dominant force of protein folding: the… (More)

- William E. Hart, Jean-Paul Watson, David L. Woodruff
- Math. Program. Comput.
- 2011

We describe Pyomo, an open source software package for modeling and solving mathematical programs in Python. Pyomo can be used to define abstract and concrete problems, create problem instances, and solve these instances with standard open-source and commercial solvers. Pyomo provides a capability that is commonly associated with algebraic modeling… (More)

- John Atkins, William E. Hart
- Algorithmica
- 1999

We describe a proof of NP-hardness for a lattice protein folding model whose instances contain protein sequences defined with a fixed, finite alphabet that contains 12 amino acid types. This lattice model represents a protein's conformation as a self-avoiding path that is embedded on the three-dimensional cubic lattice. A contact potential is used to… (More)