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1

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules

Lusci, Alessandro, Pollastri, Gianluca, Baldi, Pierre

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 2.40 MB

english, 2013

2

Improving the analysis of NMR spectra tracking pH-induced conformational changes: Removing artefacts of the electric field on the NMR chemical shift

Predrag Kukić, Damien Farrell, Chresten R. Søndergaard, Una Bjarnadottir, John Bradley, Gianluca Pollastri, Jens Erik Nielsen

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 678 KB

english, 2010

3

Deep learning methods in protein structure prediction

Le, Quan, Torrisi, Mirko, Pollastri, Gianluca

Journal:

Computational and Structural Biotechnology Journal

Year:

2020

Language:

english

File:

PDF, 1.52 MB

english, 2020

4

Learning protein secondary structure from sequential and relational data

Alessio Ceroni, Paolo Frasconi, Gianluca Pollastri

Journal:

Neural Networks

Year:

2005

Language:

english

File:

PDF, 287 KB

english, 2005

5

Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks

Ian Walsh, Davide Baù, Alberto JM Martin, Catherine Mooney, Alessandro Vullo, Gianluca Pollastri

Journal:

BMC Structural Biology

Year:

2009

Language:

english

File:

PDF, 1.50 MB

english, 2009

6

Prediction of coordination number and relative solvent accessibility in proteins

Gianluca Pollastri, Pierre Baldi, Pietro Fariselli, Rita Casadio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2002

Language:

english

File:

PDF, 228 KB

english, 2002

7

Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles

Gianluca Pollastri, Darisz Przybylski, Burkhard Rost, Pierre Baldi

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2002

Language:

english

File:

PDF, 104 KB

english, 2002

8

Beyond the Twilight Zone: Automated prediction of structural properties of proteins by recursive neural networks and remote homology information

Catherine Mooney, Gianluca Pollastri

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 357 KB

english, 2009

9

Combining protein secondary structure prediction models with ensemble methods of optimal complexity

Yann Guermeur, Gianluca Pollastri, André Elisseeff, Dominique Zelus, Hélène Paugam-Moisy, Pierre Baldi

Journal:

Year:

2004

Language:

english

File:

PDF, 358 KB

english, 2004

10

Ab initio and homology based prediction of protein domains by recursive neural networks

Ian Walsh, Alberto JM Martin, Catherine Mooney, Enrico Rubagotti, Alessandro Vullo, Gianluca Pollastri

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 571 KB

english, 2009

11

A two-stage approach for improved prediction of residue contact maps

Alessandro Vullo, Ian Walsh, Gianluca Pollastri

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 454 KB

english, 2006

12

Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins

Davide Baú, Alberto JM Martin, Catherine Mooney, Alessandro Vullo, Ian Walsh, Gianluca Pollastri

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 408 KB

english, 2006

13

Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information

Gianluca Pollastri, Alberto JM Martin, Catherine Mooney, Alessandro Vullo

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 349 KB

english, 2007

14

Structural Alphabets for Protein Structure Classification: A Comparison Study

Quan Le, Gianluca Pollastri, Patrice Koehl

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 1.19 MB

english, 2009

15

Prediction of Short Linear Protein Binding Regions

Catherine Mooney, Gianluca Pollastri, Denis C. Shields, Niall J. Haslam

Journal:

Journal of Molecular Biology

Year:

2012

Language:

english

File:

PDF, 1024 KB

english, 2012

16

Determination of Electrostatic Interaction Energies and Protonation State Populations in Enzyme Active Sites

Chresten R. Søndergaard, Lawrence P. McIntosh, Gianluca Pollastri, Jens Erik Nielsen

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 1.53 MB

english, 2008

17

Accurate prediction of protein enzymatic class by N-to-1 Neural Networks

Viola Volpato, Alessandro Adelfio, Gianluca Pollastri

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 241 KB

english, 2013

18

SCL-Epred: a generalised de novo eukaryotic protein subcellular localisation predictor

Catherine Mooney, Amélie Cessieux, Denis C. Shields, Gianluca Pollastri

Journal:

Year:

2013

Language:

english

File:

PDF, 229 KB

english, 2013

19

Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks

Kukic, Predrag, Mirabello, Claudio, Tradigo, Giuseppe, Walsh, Ian, Veltri, Pierangelo, Pollastri, Gianluca

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 864 KB

english, 2014

20

SCLpredT: Ab initio and homology-based prediction of subcellular localization by N-to-1 neural networks

Adelfio, Alessandro, Volpato, Viola, Pollastri, Gianluca

Journal:

Year:

2013

Language:

english

File:

PDF, 401 KB

english, 2013

21

Structural Artifacts in Protein−Ligand X-ray Structures: Implications for the Development of Docking Scoring Functions

Søndergaard, Chresten R., Garrett, Alison Elizabeth, Carstensen, Tommy, Pollastri, Gianluca, Nielsen, Jens Erik

Journal:

Journal of Medicinal Chemistry

Year:

2009

Language:

english

File:

PDF, 4.45 MB

english, 2009

22

[IEEE 2008 IEEE International Joint Conference on Neural Networks (IJCNN 2008 - Hong Kong) - Hong Kong, China (2008.06.1-2008.06.8)] 2008 IEEE International Joint Conference on Neural Networks (IEEE World Congress on Computational Intelligence) - A neural network approach to ordinal regression

Jianlin Cheng,, Zheng Wang,, Pollastri, Gianluca

Year:

2008

Language:

english

File:

PDF, 171 KB

english, 2008

23

Modular DAG–RNN Architectures for Assembling Coarse Protein Structures

Pollastri, Gianluca, Vullo, Alessandro, Frasconi, Paolo, Baldi, Pierre

Journal:

Journal of Computational Biology

Year:

2006

Language:

english

File:

PDF, 565 KB

english, 2006

24

Protein Structural Motif Prediction in Multidimensional ø - ψ Space Leads to Improved Secondary Structure Prediction

Mooney, Catherine, Vullo, Alessandro, Pollastri, Gianluca

Journal:

Journal of Computational Biology

Year:

2006

Language:

english

File:

PDF, 263 KB

english, 2006

25

LONG-RANGE INFORMATION AND PHYSICALITY CONSTRAINTS IMPROVE PREDICTED PROTEIN CONTACT MAPS

MARTIN, ALBERTO J. M., BAÙ, DAVIDE, VULLO, ALESSANDRO, WALSH, IAN, POLLASTRI, GIANLUCA

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2008

Language:

english

File:

PDF, 825 KB

english, 2008

26

Reconstructing Protein Structures by Neural Network Pairwise Interaction Fields and Iterative Decoy Set Construction

Mirabello, Claudio, Adelfio, Alessandro, Pollastri, Gianluca

Journal:

Year:

2014

Language:

english

File:

PDF, 667 KB

english, 2014

27

Correct machine learning on protein sequences: a peer-reviewing perspective

Walsh, Ian, Pollastri, Gianluca, Tosatto, Silvio C. E.

Journal:

Briefings in Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.25 MB

english, 2015

28

[ACM Press the 7th ACM International Conference - Seattle, WA, USA (2016.10.02-2016.10.05)] Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16 - G-quadruplex Structure Prediction and integration in the GenData2020 data model

Tradigo, Giuseppe, Cristiano, Francesca, Alcaro, Stefano, Greco, Sergio, Pollastri, Gianluca, Veltri, Pierangelo, Prosperi, Mattia

Year:

2016

Language:

english

File:

PDF, 823 KB

english, 2016

29

Towards the Improved Discovery and Design of Functional Peptides: Common Features of Diverse Classes Permit Generalized Prediction of Bioactivity

Mooney, Catherine, Haslam, Niall J., Pollastri, Gianluca, Shields, Denis C., Kurgan, Lukasz

Journal:

Year:

2012

Language:

english

File:

PDF, 697 KB

english, 2012

30

Accurate Ab Initio and Template-Based Prediction of Short Intrinsically-Disordered Regions by Bidirectional Recurrent Neural Networks Trained on Large-Scale Datasets

Volpato, Viola, Alshomrani, Badr, Pollastri, Gianluca

Journal:

International Journal of Molecular Sciences

Year:

2015

Language:

english

File:

PDF, 503 KB

english, 2015

31

Infra Red Spectroscopy of the Regulated Asbestos Amphiboles

Della Ventura, Giancarlo, Vigliaturo, Ruggero, Gieré, Reto, Pollastri, Simone, Gualtieri, Alessandro, Iezzi, Gianluca

Journal:

Year:

2018

Language:

english

File:

PDF, 2.76 MB

english, 2018

32

PaleAle 5.0: prediction of protein relative solvent accessibility by deep learning

Kaleel, Manaz, Torrisi, Mirko, Mooney, Catherine, Pollastri, Gianluca

Journal:

Year:

2019

Language:

english

File:

PDF, 836 KB

english, 2019

33

Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction

Torrisi, Mirko, Kaleel, Manaz, Pollastri, Gianluca

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 1.32 MB

english, 2019

34

SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks

Kaleel, Manaz, Zheng, Yandan, Chen, Jialiang, Feng, Xuanming, Simpson, Jeremy C, Pollastri, Gianluca, Mooney, Catherine, Martelli, Pier Luigi

Journal:

Year:

2020

File:

PDF, 855 KB

2020

35

Brewery: Deep Learning and deeper profiles for the prediction of 1D protein structure annotations

Torrisi, Mirko, Pollastri, Gianluca, Elofsson, Arne

Journal:

Year:

2020

Language:

english

File:

PDF, 146 KB

english, 2020

36

Prediction of polyproline II secondary structure propensity in proteins

OâBrien, Kevin T., Mooney, Catherine, Lopez, Cyril, Pollastri, Gianluca, Shields, Denis C.

Journal:

Royal Society Open Science

Year:

2020

File:

PDF, 457 KB

2020

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