Journal of chemical information and modeling, Jan 24, 2018
Molecular docking can account for receptor flexibility by combining the docking score over multip... more Molecular docking can account for receptor flexibility by combining the docking score over multiple rigid receptor conformations, such as snapshots from a molecular dynamics simulation. Here, we evaluate a number of common snapshot selection strategies using a quality metric from stratified sampling, the efficiency of stratification, which compares the variance of a selection strategy to simple random sampling. We also extend the metric to estimators of exponential averages (which involve an exponential transformation, averaging, and inverse transformation) and minima. For docking sets of over 500 ligands to four different proteins of varying flexibility, we observe that, for estimating ensemble averages and exponential averages, many clustering algorithms have similar performance trends: for a few snapshots (less than 25), medoids are the most efficient, while, for a larger number, optimal (the allocation that minimizes the variance) and proportional (to the size of each cluster) a...
10th International Symposium on Software Metrics, 2004. Proceedings.
Page 1. v Table of Contents 10th International Symposium on Software Metrics METRICS 2004 Forewor... more Page 1. v Table of Contents 10th International Symposium on Software Metrics METRICS 2004 Foreword from the Organizing Committee _____ ix Organizing Committee _____ x Program Committee_____ xi Keynote _____xii ...
Abstract The introduction of multiple remote testers to apply a test or checking sequence introdu... more Abstract The introduction of multiple remote testers to apply a test or checking sequence introduces the possibility of controllability and observability problems. These problems can require the use of external coordination message exchanges among testers. It is desirable ...
International Conference on Program Comprehension, 2007
Search based software engineering (SBSE) is an approach to software engineering in which search b... more Search based software engineering (SBSE) is an approach to software engineering in which search based optimization algorithms are used to identify optimal or near optimal solutions and to yield insight. SBSE techniques can cater for multiple, possibly competing objectives and/or constraints and applications where the potential solution space is large and complex. Such situations are common in software engineering, leading
Journal of chemical information and modeling, Jan 24, 2018
Molecular docking can account for receptor flexibility by combining the docking score over multip... more Molecular docking can account for receptor flexibility by combining the docking score over multiple rigid receptor conformations, such as snapshots from a molecular dynamics simulation. Here, we evaluate a number of common snapshot selection strategies using a quality metric from stratified sampling, the efficiency of stratification, which compares the variance of a selection strategy to simple random sampling. We also extend the metric to estimators of exponential averages (which involve an exponential transformation, averaging, and inverse transformation) and minima. For docking sets of over 500 ligands to four different proteins of varying flexibility, we observe that, for estimating ensemble averages and exponential averages, many clustering algorithms have similar performance trends: for a few snapshots (less than 25), medoids are the most efficient, while, for a larger number, optimal (the allocation that minimizes the variance) and proportional (to the size of each cluster) a...
10th International Symposium on Software Metrics, 2004. Proceedings.
Page 1. v Table of Contents 10th International Symposium on Software Metrics METRICS 2004 Forewor... more Page 1. v Table of Contents 10th International Symposium on Software Metrics METRICS 2004 Foreword from the Organizing Committee _____ ix Organizing Committee _____ x Program Committee_____ xi Keynote _____xii ...
Abstract The introduction of multiple remote testers to apply a test or checking sequence introdu... more Abstract The introduction of multiple remote testers to apply a test or checking sequence introduces the possibility of controllability and observability problems. These problems can require the use of external coordination message exchanges among testers. It is desirable ...
International Conference on Program Comprehension, 2007
Search based software engineering (SBSE) is an approach to software engineering in which search b... more Search based software engineering (SBSE) is an approach to software engineering in which search based optimization algorithms are used to identify optimal or near optimal solutions and to yield insight. SBSE techniques can cater for multiple, possibly competing objectives and/or constraints and applications where the potential solution space is large and complex. Such situations are common in software engineering, leading
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