E. Faraggi

发表

A superposition test for the emergence of nonlinearities in a laser irradiated spherical absorber

A. Kloczkowski, E. Faraggi, B. Gerstman, 2014, 1711.02986.

Predicting residue–residue contact maps by a two‐layer, integrated neural‐network method

Bin Xue, Yaoqi Zhou, Eshel Faraggi, 2009, Proteins.

Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

Yuedong Yang, Shesheng Zhang, Yaoqi Zhou, 2009, Structure.

Real‐value prediction of backbone torsion angles

Bin Xue, Yaoqi Zhou, Eshel Faraggi, 2008, Proteins.

Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile.

Yaoqi Zhou, A. Kloczkowski, M. Kouza, 2017, Methods in molecular biology.

Chapter 10 Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profi le

Yaoqi Zhou, A. Kloczkowski, M. Kouza, 2016 .

Protein Secondary Structure Assignments and Their Usefulness for Dihedral Angle Prediction

A. Kloczkowski, E. Faraggi, 2018, Springer Series on Bio- and Neurosystems.

Accurate Prediction of One-Dimensional Protein Structure Features Using SPINE-X.

Andrzej Kloczkowski, Eshel Faraggi, A. Kloczkowski, 2017, Methods in molecular biology.

SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method

A Keith Dunker, Vladimir N Uversky, Bin Xue, 2012, Journal of biomolecular structure & dynamics.

Fluctuations of backbone torsion angles obtained from NMR‐determined structures and their prediction

Yaoqi Zhou, Eshel Faraggi, Yaoqi Zhou, 2010, Proteins.

Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment‐based local and energy‐based nonlocal profiles

Yuedong Yang, Jian Zhan, Yaoqi Zhou, 2014, Proteins.

Trends in template/fragment-free protein structure prediction

Y. Duan, Yaoqi Zhou, Yuedong Yang, 2010, Theoretical chemistry accounts.

Acoustical resonant absorption of pulsed laser radiation by a spherical absorber

E. Faraggi, B. Gerstman, 2007 .

Biophysical effects of pulsed lasers in the retina and other tissues containing strongly absorbing particles: shockwave and explosive bubble generation.

E. Faraggi, B. Gerstman, Jinming Sun, 2005, Journal of biomedical optics.

Magnetic energy loss in permalloy thin films and microstructures

Eshel Faraggi, James L Erskine, E. Faraggi, 2005 .

Explicit solutions to phenomenological models of magnetization reversal of thin ferromagnetic films in the presence of a sawtooth magnetic field

E. Faraggi, 2006 .

Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder

A. Dunker, J. Sussman, A. Kloczkowski, 2018, Journal of biomolecular structure & dynamics.

Nonlinear Behavior in Ferromagnetism: Simple Example and Possible Implications

E. Faraggi, 2002, nlin/0209006.

Simulation of hysteresis in magnetic nanoparticles with Nosé thermostating.

L. Reichl, E. Faraggi, D. T. Robb, 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

DescribePROT: database of amino acid-level protein structure and function predictions

A Keith Dunker, Zoran Obradovic, Lukasz Kurgan, 2020, Nucleic Acids Res..

Accurate single‐sequence prediction of solvent accessible surface area using local and global features

Yaoqi Zhou, Andrzej Kloczkowski, Eshel Faraggi, 2014, Proteins.

Growing E-coli in the presence of electric fields

E. Faraggi, 2017, 1709.02745.

Symmetrical charge-charge interactions in ionic solutions: implications for biological interactions

E. Faraggi, 2012, 1201.0556.

Intrinsic Disorder and Semi-disorder Prediction by SPINE-D.

Yaoqi Zhou, Tuo Zhang, Eshel Faraggi, 2016, Methods in molecular biology.

Prediction of Protein Secondary Structure

Andrzej Kloczkowski, Yaoqi Zhou, Eshel Faraggi, 2017, Methods in Molecular Biology.

Intrinsically Semi-disordered State and Its Role in Induced Folding and Protein Aggregation

Yaoqi Zhou, Eshel Faraggi, Zhixiu Li, 2013, Cell Biochemistry and Biophysics.

BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences

Yaoqi Zhou, Lukasz Kurgan, Jianzhao Gao, 2012, PloS one.

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

Yaoqi Zhou, Yuedong Yang, Huiying Zhao, 2011, Bioinform..

SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

Lukasz A. Kurgan, Yaoqi Zhou, Yuedong Yang, 2012, J. Comput. Chem..

GENN: a GEneral Neural Network for learning tabulated data with examples from protein structure prediction.

Andrzej Kloczkowski, Eshel Faraggi, A. Kloczkowski, 2015, Methods in molecular biology.

Prediction of One‐Dimensional Structural Properties Of Proteins by Integrated Neural Networks

Yaoqi Zhou, Eshel Faraggi, Yaoqi Zhou, 2010 .

Improving the prediction accuracy of residue solvent accessibility and real‐value backbone torsion angles of proteins by guided‐learning through a two‐layer neural network

Yaoqi Zhou, Bin Xue, Eshel Faraggi, 2009, Proteins.

Magnetic behavior of partially filled finite ising surfaces

L. Reichl, E. Faraggi, D. T. Robb, 2006 .

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Adam Liwo, Yi He, Jilong Li, 2018, Scientific Reports.

The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool.

Andrzej Kloczkowski, Andrzej Kolinski, Maksim Kouza, 2017, Methods in molecular biology.

Reoptimized UNRES Potential for Protein Model Quality Assessment

Adam Liwo, Andrzej Kloczkowski, Pawel Krupa, 2018, Genes.

A global machine learning based scoring function for protein structure prediction

Andrzej Kloczkowski, Eshel Faraggi, A. Kloczkowski, 2014, Proteins.

Entropy, Fluctuations, and Disordered Proteins

Eshel Faraggi, Robert L. Jernigan, A. Keith Dunker, 2019, Entropy.

A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models

Andrzej Kloczkowski, Robert L Jernigan, Eshel Faraggi, 2020, Artificial Neural Networks, 3rd Edition.

SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

Yaoqi Zhou, Tuo Zhang, Lukasz Kurgan, 2012, J. Comput. Chem..

Resonant absorption in nanometer gold spherical particles

Eshel Faraggi, Bernard S. Gerstman, E. Faraggi, 2006, SPIE BiOS.

Accessible surface area of proteins from purely sequence information and the importance of global features

Yaoqi Zhou, Eshel Faraggi, Andrzej Kloczkowski, 2014 .

DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options

J. Söding, Martin Steinegger, M. Mirdita, 2023, Nucleic acids research.

Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A

P. Radivojac, W. Clark, R. Casadio, 2024, bioRxiv.