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Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially–Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination [chapter]

Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg
2006 Lecture Notes in Computer Science  
We develop a probabilistic hypergraph model of residue relationships that generalizes traditional pairwise contact potentials to account for the statistics of multi-residue interactions.  ...  We also use this model in optimizing site-directed recombination experiments to preserve significant interactions and thereby increase the frequency of generating useful recombinants.  ...  Bruce Craig (Statistics, Purdue), Shobha Potluri and John Thomas (CS, Dartmouth), and Michal Gajda (IIMCB, Poland) for stimulating discussion.  ... 
doi:10.1007/11732990_2 fatcat:45626ymu5bbyvek7hkfprap5by

Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination

Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg
2007 Journal of Computational Biology  
We develop a probabilistic hypergraph model of residue relationships that generalizes traditional pairwise contact potentials to account for the statistics of multi-residue interactions.  ...  We also use this model in optimizing site-directed recombination experiments to preserve significant interactions and thereby increase the frequency of generating useful recombinants.  ...  Bruce Craig (Statistics, Purdue), Shobha Potluri and John Thomas (CS, Dartmouth), and Michal Gajda (IIMCB, Poland) for stimulating discussion.  ... 
doi:10.1089/cmb.2007.r016 pmid:17691894 fatcat:ctbglk6g7ndyxoxoy4z6b7twm4

An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design [article]

Yi Zhang
2021 arXiv   pre-print
Concretely, 13 of them leverage GNN for molecular property prediction and 29 of them use RL and/or deep generative models for molecule generation and optimization.  ...  In most cases, the focus of the summary is the models, their variants, and modifications for specific tasks in drug design.  ...  The authors of this work point out that many relevant works only capture the direct interactions (referred to as direct similarity) in a molecular network for molecular interaction prediction.  ... 
arXiv:2110.05478v1 fatcat:uq2lera3znhpziuig6n44uuaby

The Vessel Schedule Recovery Problem (VSRP) – A MIP model for handling disruptions in liner shipping

Berit D. Brouer, Jakob Dirksen, David Pisinger, Christian E.M. Plum, Bo Vaaben
2013 European Journal of Operational Research  
The problem was formulated for the real packing constrains appearing in the sales and logistics departments of household equipment factory.  ...  This talk provides an overview of major modeling and computational challenges in the development of deterministic and stochastic linear/nonlinear mixedinteger optimization models for planning and scheduling  ...  -Optimal Dynamic Tax Evasion: A Portfolio Approach Francesco Menoncin, Economics, Brescia University, Via S. Faustino, 74/B, 25122, Brescia, Italy, menoncin@eco.unibs.it, Rosella Levaggi  ... 
doi:10.1016/j.ejor.2012.08.016 fatcat:c27kagfnxnhjfbil2rydhjhomm

Information Retrieval with Verbose Queries

Manish Gupta, Michael Bendersky
2015 Proceedings of the 38th International ACM SIGIR Conference on Research and Development in Information Retrieval - SIGIR '15  
In the remainder of this chapter, we will examine some of these research directions in depth. Acknowledgements We are indebted to many people for making this survey possible.  ...  retrieval models.  ...  Lord Rama breaking Molecular model for the RecBCD pathway of recombination.  ... 
doi:10.1145/2766462.2767877 dblp:conf/sigir/GuptaB15 fatcat:tgjnvqbbwfepjiggyecfaupqsa

Graph-Based Approaches to Protein StructureComparison - From Local to Global Similarity

Marco Mernberger, Mathematik Und Informatik, Hüllermeier, Eyke (Prof.)
2012
The use of graphs for the modeling of protein structure data has a long standing tradition in structural bioinformatics.  ...  Regarding the function of an enzyme, the overall fold topology might less important than the specific structural conformation of the catalytic site or the surface region of a protein, where the interaction  ...  MUSTA (Leibowitz et al., 2001) and MultiProt (Shatsky et al., 2002b) Most of these approaches constrain themselves by relying on the sequential ordering of residues.  ... 
doi:10.17192/z2012.0057 fatcat:dp6ivnp2anc5tgvwovekx5q4fq

a need to know

William A. Spencer, Larry R. Gettman, H. H. Bridge, Allan J. Ryan
1983 Physician and sportsmedicine  
on the Sphere-FPhillip Paine, University of Nottingham 10 The Orthogonally Partitioned EM Algorithm: Extending the EM Algorithm for Algorithmic Stability and Bias Correction Due to Imperfect Data-FMichael  ...  Theoretic, Algorithmic, and Empirical Issues in the Application of Directed Probabilistic Graphical Models for Network Inference When Analyzing Genomics Data-FJason Mezey, Cornell University 10:05  ...  Professional Development This year marks the centennial of Statistics of Income (SOI), a principal Federal statistical agency responsible for the statistical policies and programs of the U.S.  ... 
doi:10.1080/00913847.1983.11708423 pmid:27409254 fatcat:7rlbreoerngb3epmighz7l5vr4

Modern Applied Science, Vol. 3, No. 2, February 2009, all in one file

Editor MAS
2009 Modern Applied Science  
in the rapid decrease of sulphamethoxazole concentration level in water.  ...  over sulphamethoxazole in the presence of TiO 2 and UV.  ...  The results emphasise that for adsorption from surfactant mixtures, it is necessary to take into account the changes in the CMC with changes in composition.  ... 
doi:10.5539/mas.v3n2p0 fatcat:4bjvcqfu5jg7bbzxcjoq477gcy

Dynamical Models of biological networks

Lukas Endler
2012 unpublished
The last part describes MiniCellSim, a model of a self-contained in silico cell.  ...  In this thesis different types of gene regulatory networks are analysed using mathematical models.  ...  I learnt a lot from my supervisors Peter Schuster and Christoph Flammfrom dynamical systems analysis, over evolution to the dark intricacies of Perl programming.  ... 
doi:10.25365/thesis.22596 fatcat:u7lbhjhzujgqnhdiwqcwvackia