List of works - Amarda Shehu

A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes.

scientific article

A General, Adaptive, Roadmap-Based Algorithm for Protein Motion Computation

scientific article published on 5 February 2016

A PCA-guided Search Algorithm to Probe the Conformational Space of the Ras Protein

A basin hopping algorithm for protein-protein docking

A population-based evolutionary algorithm for sampling minima in the protein energy surface

A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction

scientific article

A robotics-inspired method to sample conformational paths connecting known functionally-relevant structures in protein systems

A tree-based search to bias sampling of protein decoy conformations

article

A two-stage evolutionary approach for effective classification of hypersensitive DNA sequences

scientific article published in June 2011

An evolutionary algorithm approach for feature generation from sequence data and its application to DNA splice site prediction

scientific article

An evolutionary conservation-based method for refining and reranking protein complex structures.

scientific article

An evolutionary framework to sample near-native protein conformations

An evolutionary search framework to efficiently sample local minima in the protein conformational space

An evolutionary-based approach for feature generation: Eukaryotic promoter recognition

Are nicotinic acetylcholine receptors coupled to G proteins?

scientific article

Attenuating dependence on structural data in computing protein energy landscapes.

scientific article published on 6 June 2019

Automated Design of Assemblable, Modular, Synthetic Chromosomes

article

Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction

Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules

scholarly article by Brian Olson et al published 2012 in Advances in Artificial Intelligence

Biased decoy sampling to aid the selection of near-native protein conformations

article

Binary Response Models for Recognition of Antimicrobial Peptides

Characterizing Energy Landscapes of Peptides Using a Combination of Stochastic Algorithms

scientific article published on 29 April 2015

Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics

scientific article published on 27 October 2015

Computational Structural Biology: Successes, Future Directions, and Challenges

Computational biologist in profile

Computing energy landscape maps and structural excursions of proteins

scientific article

Conformational Search for the Protein Native State

Data Size and Quality Matter: Generating Physically-Realistic Distance Maps of Protein Tertiary Structures

scientific article published in 2022

Deep Learning Improves Antimicrobial Peptide Recognition.

scientific article published on 24 March 2018

Effective automated feature construction and selection for classification of biological sequences

scientific article

Efficient basin hopping in the protein energy surface

Elucidating the Role of Wildtype and Variant FGFR2 Structural Dynamics in (Dys)Function and Disorder

scientific article published in 2024

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

scientific article

Evaluating Autoencoder-Based Featurization and Supervised Learning for Protein Decoy Selection

scientific article published on 04 March 2020

Evolutionary search algorithms for protein modeling

scholarly article published 2014

Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

scientific article

Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space

scientific article

Exploring the Structure Space of Wildtype Ras Guided by Experimental Data

Feature and Kernel Evolution for Recognition of Hypersensitive Sites in DNA Sequences

Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody

scientific article published in 2022

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction.

scientific article published on 19 January 2018

From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes

scientific article

From mutations to mechanisms and dysfunction via computation and mining of protein energy landscapes

Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction

Guiding probabilistic search of the protein conformational space with structural profiles

scientific article published in June 2012

Guiding protein docking with geometric and evolutionary information

scientific article published in June 2012

Higher-order representations of protein structure space

HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking

scientific article published on 7 November 2013

Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming.

scientific article published in March 2017

In search of the protein native state with a probabilistic sampling approach

scientific article

Informatics-driven Protein-protein Docking

Jumping low, jumping high: Controlling hopping in the protein energy surface

Mapping conformational pathways between known functional protein states

Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm

scientific article published on September 2015

Menthol binding and inhibition of α7-nicotinic acetylcholine receptors

scientific article (publication date: 2013)

Menthol inhibits 5-HT3 receptor-mediated currents

scientific article

Modeling Structures and Motions of Loops in Protein Molecules

article

Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations.

scientific article published in October 2006

Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy Surface

Multiscale characterization of protein conformational ensembles

scientific article published on September 2009

Off-lattice protein structure prediction with homologous crossover

On the characterization of protein native state ensembles

scientific article published on 8 December 2006

Physico-chemical features for recognition of antimicrobial peptides

Populating Local Minima in the Protein Conformational Space

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

scientific article

Probabilistic search and energy guidance for biased decoy sampling in ab initio protein structure prediction.

scientific article

Protein-protein Docking Using Information from Native Interaction Interfaces

Rapid sampling of local minima in protein energy surface and effective reduction through a multi-objective filter

scientific article published on 7 November 2013

Reducing Ensembles of Protein Tertiary Structures Generated De Novo via Clustering

scientific article published on 09 May 2020

Restriction versus guidance in protein structure prediction.

scientific article

Sample-Based Models of Protein Energy Landscapes and Slow Structural Rearrangements

scientific article published on 15 November 2017

Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins

article

Sampling low-energy protein-protein configurations with basin hopping

Sampling-based methods for a full characterization of energy landscapes of small peptides

Selecting predictive features for recognition of hypersensitive sites of regulatory genomic sequences with an evolutionary algorithm

Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm

scientific article

Systematic analysis of global features and model building for recognition of antimicrobial peptides

article

The 5th International Conference on Bio-Inspired Models of Network, Information and Computing Systems (BIONETICS 2010) special track on bioinformatics.

scientific article published in June 2011

The 6th Computational Structural Bioinformatics Workshop

scientific article published on 8 November 2013

The 7th Computational Structural Bioinformatics Workshop

scientific article

The AAAI-13 Conference Workshops

Unfolding the fold of cyclic cysteine-rich peptides

scientific article

Unsupervised and Supervised Learning over theEnergy Landscape for Protein Decoy Selection

scientific article published on 14 October 2019

Using evolutionary computation to improve SVM classification

idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking

scientific article

List of works by Amarda Shehu

A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes.

A General, Adaptive, Roadmap-Based Algorithm for Protein Motion Computation

A PCA-guided Search Algorithm to Probe the Conformational Space of the Ras Protein

A basin hopping algorithm for protein-protein docking

A population-based evolutionary algorithm for sampling minima in the protein energy surface

A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction

A robotics-inspired method to sample conformational paths connecting known functionally-relevant structures in protein systems

A tree-based search to bias sampling of protein decoy conformations

A two-stage evolutionary approach for effective classification of hypersensitive DNA sequences

An evolutionary algorithm approach for feature generation from sequence data and its application to DNA splice site prediction

An evolutionary conservation-based method for refining and reranking protein complex structures.

An evolutionary framework to sample near-native protein conformations

An evolutionary search framework to efficiently sample local minima in the protein conformational space

An evolutionary-based approach for feature generation: Eukaryotic promoter recognition

Are nicotinic acetylcholine receptors coupled to G proteins?

Attenuating dependence on structural data in computing protein energy landscapes.

Automated Design of Assemblable, Modular, Synthetic Chromosomes

Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction

Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules

Biased decoy sampling to aid the selection of near-native protein conformations

Binary Response Models for Recognition of Antimicrobial Peptides

Characterizing Energy Landscapes of Peptides Using a Combination of Stochastic Algorithms

Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics

Computational Structural Biology: Successes, Future Directions, and Challenges

Computational biologist in profile

Computing energy landscape maps and structural excursions of proteins

Conformational Search for the Protein Native State

Data Size and Quality Matter: Generating Physically-Realistic Distance Maps of Protein Tertiary Structures

Deep Learning Improves Antimicrobial Peptide Recognition.

Effective automated feature construction and selection for classification of biological sequences

Efficient basin hopping in the protein energy surface

Elucidating the Role of Wildtype and Variant FGFR2 Structural Dynamics in (Dys)Function and Disorder

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

Evaluating Autoencoder-Based Featurization and Supervised Learning for Protein Decoy Selection

Evolutionary search algorithms for protein modeling

Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space

Exploring the Structure Space of Wildtype Ras Guided by Experimental Data

Feature and Kernel Evolution for Recognition of Hypersensitive Sites in DNA Sequences

Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction.

From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes

From mutations to mechanisms and dysfunction via computation and mining of protein energy landscapes

Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction

Guiding probabilistic search of the protein conformational space with structural profiles

Guiding protein docking with geometric and evolutionary information

Higher-order representations of protein structure space

HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking

Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming.

In search of the protein native state with a probabilistic sampling approach

Informatics-driven Protein-protein Docking

Jumping low, jumping high: Controlling hopping in the protein energy surface

Mapping conformational pathways between known functional protein states

Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm

Menthol binding and inhibition of α7-nicotinic acetylcholine receptors

Menthol inhibits 5-HT3 receptor-mediated currents

Modeling Structures and Motions of Loops in Protein Molecules

Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations.

Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy Surface

Multiscale characterization of protein conformational ensembles

Off-lattice protein structure prediction with homologous crossover

On the characterization of protein native state ensembles

Physico-chemical features for recognition of antimicrobial peptides

Populating Local Minima in the Protein Conformational Space

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

Probabilistic search and energy guidance for biased decoy sampling in ab initio protein structure prediction.

Protein-protein Docking Using Information from Native Interaction Interfaces

Rapid sampling of local minima in protein energy surface and effective reduction through a multi-objective filter

Reducing Ensembles of Protein Tertiary Structures Generated De Novo via Clustering

Restriction versus guidance in protein structure prediction.

Sample-Based Models of Protein Energy Landscapes and Slow Structural Rearrangements

Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins

Sampling low-energy protein-protein configurations with basin hopping

Sampling-based methods for a full characterization of energy landscapes of small peptides

Selecting predictive features for recognition of hypersensitive sites of regulatory genomic sequences with an evolutionary algorithm

Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm

Systematic analysis of global features and model building for recognition of antimicrobial peptides

The 5th International Conference on Bio-Inspired Models of Network, Information and Computing Systems (BIONETICS 2010) special track on bioinformatics.

The 6th Computational Structural Bioinformatics Workshop