Works by SHEHU, AMARDA

Results: 54

An Energy Landscape Treatment of Decoy Selection in Template-Free Protein Structure Prediction.

Published in:

Computation, 2018, v. 6, n. 2, p. 39, doi. 10.3390/computation6020039

By:

Akhter, Nasrin;
Qiao, Wanli;
Shehu, Amarda

Publication type:

Article

Examining DNA breathing with pyDNA-EPBD.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad699

By:

Kabir, Anowarul;
Bhattarai, Manish;
Rasmussen, Kim Ø;
Shehu, Amarda;
Usheva, Anny;
Bishop, Alan R;
Alexandrov, Boian

Publication type:

Article

Small molecule generation via disentangled representation learning.

Published in:

Bioinformatics, 2022, v. 38, n. 12, p. 3200, doi. 10.1093/bioinformatics/btac296

By:

Du, Yuanqi;
Guo, Xiaojie;
Wang, Yinkai;
Shehu, Amarda;
Zhao, Liang

Publication type:

Article

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

Published in:

Proteins, 2006, v. 65, n. 1, p. 164, doi. 10.1002/prot.21060

By:

Shehu, Amarda;
Clementi, Cecilia;
Kavraki, Lydia E.

Publication type:

Article

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

Published in:

International Journal of Molecular Sciences, 2024, v. 25, n. 8, p. 4523, doi. 10.3390/ijms25084523

By:

Lian, Yiyang;
Bodian, Dale;
Shehu, Amarda

Publication type:

Article

Attenuating dependence on structural data in computing protein energy landscapes.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 11, p. 1, doi. 10.1186/s12859-019-2822-5

By:

Morris, David;
Maximova, Tatiana;
Plaku, Erion;
Shehu, Amarda

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2794-5

By:

Zaman, Ahmed Bin;
Shehu, Amarda

Publication type:

Article

Unfolding the fold of cyclic cysteine-rich peptides.

Published in:

Protein Science: A Publication of the Protein Society, 2008, v. 17, n. 3, p. 482, doi. 10.1110/ps.073142708

By:

Shehu, Amarda;
Kavraki, Lydia E.;
Clementi, Cecilia

Publication type:

Article

Foreword on special issue on robotics methods for structural and dynamic modeling of molecular systems.

Published in:

Robotica, 2016, v. 34, n. 8, p. 1677, doi. 10.1017/S0263574716000370

By:

Tapia, Lydia;
Cortés, Juan;
Shehu, Amarda;
Chen, Jinalin

Publication type:

Article

A stochastic roadmap method to model protein structural transitions.

Published in:

Robotica, 2016, v. 34, n. 8, p. 1705, doi. 10.1017/S0263574715001058

By:

Molloy, Kevin;
Clausen, Rudy;
Shehu, Amarda

Publication type:

Article

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

Published in:

Proteome Science, 2012, v. 10, n. Suppl 1, p. 1, doi. 10.1186/1477-5956-10-S1-S5

By:

Olson, Brian S.;
Shehu, Amarda

Publication type:

Article

Are nicotinic acetylcholine receptors coupled to G proteins?

Published in:

BioEssays, 2013, v. 35, n. 12, p. 1025, doi. 10.1002/bies.201300082

By:

Kabbani, Nadine;
Nordman, Jacob C.;
Corgiat, Brian A.;
Veltri, Daniel P.;
Shehu, Amarda;
Seymour, Victoria A.;
Adams, David J.

Publication type:

Article

Multiscale characterization of protein conformational ensembles.

Published in:

Proteins, 2009, v. 76, n. 4, p. 837, doi. 10.1002/prot.22390

By:

Shehu, Amarda;
Kavraki, Lydia E.;
Clementi, Cecilia

Publication type:

Article

Modeling Structures and Motions of Loops in Protein Molecules.

Published in:

Entropy, 2012, v. 14, n. 2, p. 252, doi. 10.3390/e14020252

By:

Shehu, Amarda;
Kavraki, Lydia E.

Publication type:

Article

In the twilight zone of protein sequence homology: do protein language models learn protein structure?

Published in:

Bioinformatics Advances, 2024, v. 4, n. 1, p. 1, doi. 10.1093/bioadv/vbae119

By:

Kabir, Anowarul;
Moldwin, Asher;
Bromberg, Yana;
Shehu, Amarda

Publication type:

Article

Generating tertiary protein structures via interpretable graph variational autoencoders.

Published in:

Bioinformatics Advances, 2021, v. 1, n. 1, p. 1, doi. 10.1093/bioadv/vbab036

By:

Xiaojie Guo;
Yuanqi Du;
Tadepalli, Sivani;
Liang Zhao;
Shehu, Amarda

Publication type:

Article

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

Published in:

Biomolecules (2218-273X), 2022, v. 12, n. 7, p. N.PAG, doi. 10.3390/biom12071011

By:

Kabir, Kazi Lutful;
Ma, Buyong;
Nussinov, Ruth;
Shehu, Amarda

Publication type:

Article

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

Published in:

Biomolecules (2218-273X), 2022, v. 12, n. 7, p. N.PAG, doi. 10.3390/biom12070908

By:

Alam, Fardina Fathmiul;
Shehu, Amarda

Publication type:

Article

Computing the Structural Dynamics of RVFV L Protein Domain in Aqueous Glycerol Solutions.

Published in:

Biomolecules (2218-273X), 2021, v. 11, n. 10, p. 1427, doi. 10.3390/biom11101427

By:

Gogovi, Gideon K.;
Silayi, Swabir;
Shehu, Amarda

Publication type:

Article

Unsupervised and Supervised Learning over the Energy Landscape for Protein Decoy Selection.

Published in:

Biomolecules (2218-273X), 2019, v. 9, n. 10, p. 607, doi. 10.3390/biom9100607

By:

Akhter, Nasrin;
Chennupati, Gopinath;
Kabir, Kazi Lutful;
Djidjev, Hristo;
Shehu, Amarda

Publication type:

Article

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

Published in:

Advances in Artificial Intelligence (16877470), 2012, p. 1, doi. 10.1155/2012/674832

By:

Olson, Brian;
Hashmi, Irina;
Molloy, Kevin;
Shehu, Amarda

Publication type:

Article

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

Published in:

BMC Structural Biology, 2013, v. 13, p. 1, doi. 10.1186/1472-6807-13-S1-S8

By:

Molloy, Kevin;
Shehu, Amarda

Publication type:

Article

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

Published in:

BMC Structural Biology, 2013, v. 13, p. 1, doi. 10.1186/1472-6807-13-S1-S4

By:

Saleh, Sameh;
Olson, Brian;
Shehu, Amarda

Publication type:

Article

The 6th Computational Structural Bioinformatics Workshop.

Published in:

BMC Structural Biology, 2013, v. 13, p. 1, doi. 10.1186/1472-6807-13-S1-I1

By:

Jing He;
Shehu, Amarda;
Haspel, Nurit;
Brian Chen

Publication type:

Article

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

Published in:

BMC Genomics, 2018, v. 19, p. 1, doi. 10.1186/s12864-018-5024-z

By:

Qiao, Wanli;
Akhter, Nasrin;
Fang, Xiaowen;
Maximova, Tatiana;
Shehu, Amarda;
Plaku, Erion

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2014, v. 15, n. Suppl 8, p. 1, doi. 10.1186/1471-2105-15-S8-S4

By:

Molloy, Kevin;
Jennifer Van, M.;
Barbara, Daniel;
Shehu, Amarda

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2016, v. 12, n. 4, p. 1, doi. 10.1371/journal.pcbi.1004619

By:

Maximova, Tatiana;
Moffatt, Ryan;
Ma, Buyong;
Nussinov, Ruth;
Shehu, Amarda

Publication type:

Article

Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics.

Published in:

2015

By:

Shehu, Amarda;
Nussinov, Ruth

Publication type:

Editorial

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

Published in:

PLoS Computational Biology, 2015, v. 11, n. 9, p. 1, doi. 10.1371/journal.pcbi.1004470

By:

Clausen, Rudy;
Ma, Buyong;
Nussinov, Ruth;
Shehu, Amarda

Publication type:

Article

Unsupervised multi-instance learning for protein structure determination.

Published in:

Journal of Bioinformatics & Computational Biology, 2021, v. 19, n. 1, p. N.PAG, doi. 10.1142/S0219720021400023

By:

Alam, Fardina Fathmiul;
Shehu, Amarda

Publication type:

Article

From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state models.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 6, p. N.PAG, doi. 10.1142/S0219720019400146

By:

Kabir, Kazi Lutful;
Akhter, Nasrin;
Shehu, Amarda

Publication type:

Article

Building maps of protein structure spaces in template-free protein structure prediction.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 6, p. N.PAG, doi. 10.1142/S0219720019400134

By:

Zaman, Ahmed Bin;
Shehu, Amarda

Publication type:

Article

AN EVOLUTIONARY CONSERVATION-BASED METHOD FOR REFINING AND RERANKING PROTEIN COMPLEX STRUCTURES.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 3, p. 1242002-1, doi. 10.1142/S0219720012420024

By:

AKBAL-DELIBAS, BAHAR;
HASHMI, IRINA;
SHEHU, AMARDA;
HASPEL, NURIT

Publication type:

Article

GUIDING PROBABILISTIC SEARCH OF THE PROTEIN CONFORMATIONAL SPACE WITH STRUCTURAL PROFILES.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 3, p. 1242005-1, doi. 10.1142/S021972001242005X

By:

OLSON, BRIAN;
MOLLOY, KEVIN;
HENDI, S. FARID;
SHEHU, AMARDA

Publication type:

Article

GUIDING PROTEIN DOCKING WITH GEOMETRIC AND EVOLUTIONARY INFORMATION.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 3, p. 1242008-1, doi. 10.1142/S0219720012420085

By:

HASHMI, IRINA;
AKBAL-DELIBAS, BAHAR;
HASPEL, NURIT;
SHEHU, AMARDA

Publication type:

Article

IN SEARCH OF THE PROTEIN NATIVE STATE WITH A PROBABILISTIC SAMPLING APPROACH.

Published in:

Journal of Bioinformatics & Computational Biology, 2011, v. 9, n. 3, p. 383, doi. 10.1142/S0219720011005574

By:

OLSON, BRIAN;
MOLLOY, KEVIN;
SHEHU, AMARDA

Publication type:

Article

A TWO-STAGE EVOLUTIONARY APPROACH FOR EFFECTIVE CLASSIFICATION OF HYPERSENSITIVE DNA SEQUENCES.

Published in:

Journal of Bioinformatics & Computational Biology, 2011, v. 9, n. 3, p. 399, doi. 10.1142/S0219720011005586

By:

KAMATH, UDAY;
SHEHU, AMARDA;
DE JONG, KENNETH A.

Publication type:

Article

THE 5TH INTERNATIONAL CONFERENCE ON BIO-INSPIRED MODELS OF NETWORK, INFORMATION AND COMPUTING SYSTEMS (BIONETICS 2010) SPECIAL TRACK ON BIOINFORMATICS.

Published in:

Journal of Bioinformatics & Computational Biology, 2011, v. 9, n. 3, p. v, doi. 10.1142/S0219720011005616

By:

HASPEL, NURIT;
SHEHU, AMARDA

Publication type:

Article

DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 19, p. e91, doi. 10.1093/nar/gkae783

By:

Kabir, Anowarul;
Bhattarai, Manish;
Peterson, Selma;
Najman-Licht, Yonatan;
Rasmussen, Kim Ø;
Shehu, Amarda;
Bishop, Alan R;
Alexandrov, Boian;
Usheva, Anny

Publication type:

Article

Effective Automated Feature Construction and Selection for Classification of Biological Sequences.

Published in:

PLoS ONE, 2014, v. 9, n. 7, p. 1, doi. 10.1371/journal.pone.0099982

By:

Kamath, Uday;
De Jong, Kenneth;
Shehu, Amarda

Publication type:

Article

Menthol Binding and Inhibition of α7-Nicotinic Acetylcholine Receptors.

Published in:

PLoS ONE, 2013, v. 8, n. 7, p. 1, doi. 10.1371/journal.pone.0067674

By:

Ashoor, Abrar;
Nordman, Jacob C.;
Veltri, Daniel;
Yang, Keun-Hang Susan;
Al Kury, Lina;
Shuba, Yaroslav;
Mahgoub, Mohamed;
Howarth, Frank C.;
Sadek, Bassem;
Shehu, Amarda;
Kabbani, Nadine;
Oz, Murat

Publication type:

Article

Entangled Narratives: Insights from Social and Computer Sciences on National Artificial Intelligence Infrastructures.

Published in:

International Studies Quarterly, 2025, v. 69, n. 1, p. 1, doi. 10.1093/isq/sqaf001

By:

Singh, J P;
Shehu, Amarda;
Dua, Manpriya;
Wesson, Caroline

Publication type:

Article

Computing energy landscape maps and structural excursions of proteins.

Published in:

BMC Genomics, 2016, v. 17, p. 433, doi. 10.1186/s12864-016-2798-8

By:

Sapin, Emmanuel;
Carr, Daniel B.;
De Jong, Kenneth A.;
Shehu, Amarda

Publication type:

Article

FragNet, a Contrastive Learning-Based Transformer Model for Clustering, Interpreting, Visualizing, and Navigating Chemical Space.

Published in:

Molecules, 2021, v. 26, n. 7, p. 2065, doi. 10.3390/molecules26072065

By:

Shrivastava, Aditya Divyakant;
Kell, Douglas B.;
Shehu, Amarda

Publication type:

Article

Generative Adversarial Learning of Protein Tertiary Structures.

Published in:

Molecules, 2021, v. 26, n. 5, p. 1209, doi. 10.3390/molecules26051209

By:

Rahman, Taseef;
Du, Yuanqi;
Zhao, Liang;
Shehu, Amarda;
Gascón, José A.

Publication type:

Article

Molecular Image-Based Prediction Models of Nuclear Receptor Agonists and Antagonists Using the DeepSnap-Deep Learning Approach with the Tox21 10K Library.

Published in:

Molecules, 2020, v. 25, n. 12, p. 2764, doi. 10.3390/molecules25122764

By:

Matsuzaka, Yasunari;
Uesawa, Yoshihiro;
Shehu, Amarda;
Zhao, Liang;
McPhee, Derek J.

Publication type:

Article

Reducing Ensembles of Protein Tertiary Structures Generated De Novo via Clustering.

Published in:

Molecules, 2020, v. 25, n. 9, p. 2228, doi. 10.3390/molecules25092228

By:

Zaman, Ahmed Bin;
Kamranfar, Parastoo;
Domeniconi, Carlotta;
Shehu, Amarda

Publication type:

Article

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

Published in:

Molecules, 2020, v. 25, n. 5, p. 1146, doi. 10.3390/molecules25051146

By:

Alam, Fardina Fathmiul;
Rahman, Taseef;
Shehu, Amarda

Publication type:

Article

Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein.

Published in:

Molecules, 2019, v. 24, n. 9, p. 1768, doi. 10.3390/molecules24091768

By:

Gogovi, Gideon K.;
Almsned, Fahad;
Bracci, Nicole;
Kehn-Hall, Kylene;
Shehu, Amarda;
Blaisten-Barojas, Estela;
Jagodzinski, Filip;
Chen, Brian Y.;
Torrens, Francisco

Publication type:

Article

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

Published in:

Molecules, 2019, v. 24, n. 5, p. 854, doi. 10.3390/molecules24050854

By:

Kabir, Kazi Lutful;
Hassan, Liban;
Rajabi, Zahra;
Akhter, Nasrin;
Shehu, Amarda

Publication type:

Article