Publications by authors named "Mark Moll"

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HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy.
Dinler A Antunes, Jayvee R Abella, Sarah Hall-Swan, Didier Devaurs, Anja Conev, Mark Moll, Gregory Lizée, Lydia E Kavraki

JCO Clin Cancer Inform· July 2020

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Improving the organization and interactivity of metabolic pathfinding with precomputed pathways.
Sarah M Kim, Matthew I Peña, Mark Moll, George N Bennett, Lydia E Kavraki

BMC Bioinformatics· January 2020

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Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins.
Didier Devaurs, Dinler A Antunes, Sarah Hall-Swan, Nicole Mitchell, Mark Moll

BMC Mol Cell Biol· September 2019

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Machine Learning Guided Atom Mapping of Metabolic Reactions.
Eleni E Litsa, Matthew I Peña, Mark Moll, George Giannakopoulos, George N Bennett

J Chem Inf Model· March 2019

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General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept.
Dinler A Antunes, Didier Devaurs, Mark Moll, Gregory Lizée, Lydia E Kavraki

Sci Rep· March 2018

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Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling.
Didier Devaurs, Malvina Papanastasiou, Dinler A Antunes, Jayvee R Abella, Mark Moll

Int J Comput Biol Drug Des· March 2018

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Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.
Jayvee R Abella, Mark Moll, Lydia E Kavraki

J Comput Biol· January 2018

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DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach.
Dinler A Antunes, Mark Moll, Didier Devaurs, Kyle R Jackson, Gregory Lizée

Cancer Res· November 2017

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A review of parameters and heuristics for guiding metabolic pathfinding.
Sarah M Kim, Matthew I Peña, Mark Moll, George N Bennett, Lydia E Kavraki

J Cheminform· September 2017

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Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.
Didier Devaurs, Dinler A Antunes, Malvina Papanastasiou, Mark Moll, Daniel Ricklin

Front Mol Biosci· March 2017

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Defining Low-Dimensional Projections to Guide Protein Conformational Sampling.
Anastasia Novinskaya, Didier Devaurs, Mark Moll, Lydia E Kavraki

J Comput Biol· January 2017

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Structure-guided selection of specificity determining positions in the human Kinome.
Mark Moll, Paul W Finn, Lydia E Kavraki

BMC Genomics· August 2016

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SIMS: a hybrid method for rapid conformational analysis.
Bryant Gipson, Mark Moll, Lydia E Kavraki

PLoS One· March 2014

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Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome.
Drew H Bryant, Mark Moll, Paul W Finn, Lydia E Kavraki

PLoS Comput Biol· January 2014

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The LabelHash server and tools for substructure-based functional annotation.
Mark Moll, Drew H Bryant, Lydia E Kavraki

Bioinformatics· August 2011

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The LabelHash algorithm for substructure matching.
Mark Moll, Drew H Bryant, Lydia E Kavraki

BMC Bioinformatics· November 2010

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Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction.
Drew H Bryant, Mark Moll, Brian Y Chen, Viacheslav Y Fofanov, Lydia E Kavraki

BMC Bioinformatics· May 2010

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Tracing conformational changes in proteins.
Nurit Haspel, Mark Moll, Matthew L Baker, Wah Chiu, Lydia E Kavraki

BMC Struct Biol· May 2010

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Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction.
Mark Moll, Lydia E Kavraki

Comput Syst Bioinformatics Conf· August 2009

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Roadmap methods for protein folding.
Mark Moll, David Schwarz, Lydia E Kavraki

Methods Mol Biol· June 2008

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Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction.
Payel Das, Mark Moll, Hernán Stamati, Lydia E Kavraki, Cecilia Clementi

Proc Natl Acad Sci U S A· June 2006

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Convergence-Zone Episodic Memory: Analysis and Simulations.
Risto Miikkulainen, Mark Moll

Neural Netw· August 1997

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