Publications by authors named "Ryan Lilien"

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Commentary on: Gutierrez RE, Prokesch EJ. The false promise of firearms examination validation studies: Lay controls, simplistic comparisons, and the failure to soundly measure misidentification rates. J Forensic Sci. 2024;69(4):1334-9. https://doi.org/10.1111/1556-4029.15531.
Todd J Weller, Pierre Duez MASc, Ryan Lilien

J Forensic Sci· January 2025

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Results of the 3D Virtual Comparison Microscopy Error Rate (VCMER) Study for firearm forensics.
Chad Chapnick, Todd J Weller, Pierre Duez, Eric Meschke, John Marshall, Ryan Lilien

J Forensic Sci· March 2021

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Development and Validation of a Virtual Examination Tool for Firearm Forensics,
Pierre Duez, Todd Weller, Marcus Brubaker, Richard E Hockensmith, Ryan Lilien

J Forensic Sci· July 2018

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Clinical Prediction Rule for Patient Outcome after In-Hospital CPR: A New Model, Using Characteristics Present at Hospital Admission, to Identify Patients Unlikely to Benefit from CPR after In-Hospital Cardiac Arrest.
Satyam Merja, Ryan H Lilien, Hilary F Ryder

Palliat Care· October 2015

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OSPREY: protein design with ensembles, flexibility, and provable algorithms.
Pablo Gainza, Kyle E Roberts, Ivelin Georgiev, Ryan H Lilien, Daniel A Keedy

Methods Enzymol· August 2013

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Efficient a priori identification of drug resistant mutations using Dead-End Elimination and MM-PBSA.
Maria Safi, Ryan H Lilien

J Chem Inf Model· June 2012

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Applying medicinal chemistry transformations and multiparameter optimization to guide the search for high-quality leads and candidates.
Matthew Segall, Ed Champness, Chris Leeding, Ryan Lilien, Ramgopal Mettu

J Chem Inf Model· November 2011

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Normalizing molecular docking rankings using virtually generated decoys.
Izhar Wallach, Navdeep Jaitly, Kong Nguyen, Matthieu Schapira, Ryan Lilien

J Chem Inf Model· August 2011

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Virtual decoy sets for molecular docking benchmarks.
Izhar Wallach, Ryan Lilien

J Chem Inf Model· February 2011

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A Bayesian method for 3D macromolecular structure inference using class average images from single particle electron microscopy.
Navdeep Jaitly, Marcus A Brubaker, John L Rubinstein, Ryan H Lilien

Bioinformatics· October 2010

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LigAlign: flexible ligand-based active site alignment and analysis.
Abraham Heifets, Ryan H Lilien

J Mol Graph Model· August 2010

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A structure-based approach for mapping adverse drug reactions to the perturbation of underlying biological pathways.
Izhar Wallach, Navdeep Jaitly, Ryan Lilien

PLoS One· August 2010

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Restricted dead-end elimination: protein redesign with a bounded number of residue mutations.
Maria Safi, Ryan H Lilien

J Comput Chem· April 2010

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Predicting multiple ligand binding modes using self-consistent pharmacophore hypotheses.
Izhar Wallach, Ryan Lilien

J Chem Inf Model· September 2009

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Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation.
Izhar Wallach, Ryan H Lilien

Bioinformatics· June 2009

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The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding.
Izhar Wallach, Ryan Lilien

Bioinformatics· March 2009

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The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles.
Ivelin Georgiev, Ryan H Lilien, Bruce R Donald

J Comput Chem· July 2008

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Allosteric inhibition of the protein-protein interaction between the leukemia-associated proteins Runx1 and CBFbeta.
Michael J Gorczynski, Jolanta Grembecka, Yunpeng Zhou, Yali Kong, Liya Roudaia, Ryan Lilien

Chem Biol· October 2007

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Redesigning the PheA domain of gramicidin synthetase leads to a new understanding of the enzyme's mechanism and selectivity.
Brian W Stevens, Ryan H Lilien, Ivelin Georgiev, Bruce R Donald, Amy C Anderson

Biochemistry· December 2006

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Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design.
Ivelin Georgiev, Ryan H Lilien, Bruce R Donald

Bioinformatics· July 2006

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A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme.
Ryan H Lilien, Brian W Stevens, Amy C Anderson, Bruce R Donald

J Comput Biol· October 2005

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High-throughput inference of protein-protein interfaces from unassigned NMR data.
Ramgopal R Mettu, Ryan H Lilien, Bruce Randall Donald

Bioinformatics· June 2005

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Optimization and dynamics of protein-protein complexes using B-splines.
Richard E Gillilan, Ryan H Lilien

J Comput Chem· October 2004

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A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments.
Christopher James Langmead, Anthony Yan, Ryan Lilien, Lincong Wang, Bruce Randall Donald

J Comput Biol· August 2004

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A subgroup algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry.
Ryan H Lilien, Chris Bailey-Kellogg, Amy C Anderson, Bruce R Donald

Acta Crystallogr D Biol Crystallogr· June 2004

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