Helmer-Citterich, Manuela: search on Z-Library

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1

Structural motifs recurring in different folds recognize the same ligand fragments

Gabriele Ausiello, Federico Pier Gherardini, Elena Gatti, Ottaviano Incani, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.78 MB

english, 2009

2

WWP1 germline variants are associated with normocephalic autism spectrum disorder

Novelli, Giuseppe, Novelli, Antonio, Borgiani, Paola, Cocciadiferro, Dario, Biancolella, Michela, Agolini, Emanuele, Pietrosanto, Marco, Casalone, Rosario, Helmer-Citterich, Manuela, Giardina, Emilian

Journal:

Cell Death and Disease

Year:

2020

File:

PDF, 325 KB

2020

3

MINT: a Molecular INTeraction database

Andreas Zanzoni, Luisa Montecchi-Palazzi, Michele Quondam, Gabriele Ausiello, Manuela Helmer-Citterich, Gianni Cesareni

Journal:

Year:

2002

Language:

english

File:

PDF, 410 KB

english, 2002

4

Three-dimensional profiles: a new tool to identify protein surface similarities

Manuel de Rinaldis, Gabriele Ausiello, Gianni Cesareni, Manuela Helmer-Citterich

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 429 KB

english, 1998

5

A Simple Extension to the CMASA Method for the Prediction of Catalytic Residues in the Presence of Single Point Mutations

Flores, David I., Sotelo-Mundo, Rogerio R., Brizuela, Carlos A., Helmer-Citterich, Manuela

Journal:

Year:

2014

Language:

english

File:

PDF, 1.72 MB

english, 2014

6

3D similarities between the binding sites of monoaminergic target proteins

Núñez-Vivanco, Gabriel, Fierro, Angélica, Moya, Pablo, Iturriaga-Vásquez, Patricio, Reyes-Parada, Miguel, Helmer-Citterich, Manuela

Journal:

Year:

2018

Language:

english

File:

PDF, 21.15 MB

english, 2018

7

Correlated mutations contain information about protein-protein interaction

Florencio Pazos, Manuela Helmer-Citterich, Gabriele Ausiello, Alfonso Valencia

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 475 KB

english, 1997

8

Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana

Hazarika, Rashmi R., Sostaric, Nikolina, Sun, Yifeng, van Noort, Vera, Helmer-Citterich, Manuela

Journal:

Year:

2018

Language:

english

File:

PDF, 1.46 MB

english, 2018

9

Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics

Graziano Pesole, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 187 KB

english, 2008

10

Cyclosporin A Treatment of Leishmania donovani Reveals Stage-Specific Functions of Cyclophilins in Parasite Proliferation and Viability

Yau, Wai-Lok, Blisnick, Thierry, Taly, Jean-François, Helmer-Citterich, Manuela, Schiene-Fischer, Cordelia, Leclercq, Olivier, Li, Jing, Schmidt-Arras, Dirk, Morales, Miguel A., Notredame, Cedric, Rom

Journal:

PLoS Neglected Tropical Diseases

Year:

2010

Language:

english

File:

PDF, 1.22 MB

english, 2010

11

Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells

Tabolacci, Elisabetta, Mancano, Giorgia, Lanni, Stella, Palumbo, Federica, Goracci, Martina, Ferrè, Fabrizio, Helmer-Citterich, Manuela, Neri, Giovanni

Journal:

Epigenetics & Chromatin

Year:

2016

Language:

english

File:

PDF, 1.95 MB

english, 2016

12

Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics

Facchiano, Angelo, Angelini, Claudia, Bosotti, Roberta, Guffanti, Alessandro, Marabotti, Anna, Marangoni, Roberto, Pascarella, Stefano, Romano, Paolo, Zanzoni, Andreas, Helmer-Citterich, Manuela

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 270 KB

english, 2015

13

iSPOT: a web tool for the analysis and recognition of protein domain specificity : A presentation for the ESF workshop ‘Proteomics: Focus on Protein Interactions’

Barbara Brannetti, Andreas Zanzoni, Luisa Montecchi-Palazzi, Gianni Cesareni, Manuela Helmer-Citterich

Journal:

Comparative and Functional Genomics

Year:

2001

Language:

english

File:

PDF, 221 KB

english, 2001

14

False occurrences of functional motifs in protein sequences highlight evolutionary constraints

Allegra Via, Federico Pier Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 429 KB

english, 2007

15

PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae

Antonio Palmeri, Pier Federico Gherardini, Polina Tsigankov, Gabriele Ausiello, Gerald F Späth, Dan Zilberstein, Manuela Helmer-Citterich

Journal:

Year:

2011

Language:

english

File:

PDF, 309 KB

english, 2011

16

The SH3 domain of nebulin binds selectively to type II peptides: theoretical prediction and experimental validation

Anastasia S. Politou, Roberta Spadaccini, Catherine Joseph, Barbara Brannetti, Remo Guerrini, Manuela Helmer-Citterich, Severo Salvadori, Piero Andrea Temussi, Annalisa Pastore

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 321 KB

english, 2002

17

Exploiting holistic approaches to model specificity in protein phosphorylation

Palmeri, Antonio, FerrÃ¨, Fabrizio, Helmer-Citterich, Manuela

Journal:

Frontiers in Genetics

Year:

2014

Language:

english

File:

PDF, 1.58 MB

english, 2014

18

DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach

Wang, Zhiheng, Yang, Qianqian, Li, Tonghua, Cong, Peisheng, Helmer-Citterich, Manuela

Journal:

Year:

2015

Language:

english

File:

PDF, 1.42 MB

english, 2015

19

Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites

Gabriele Ausiello, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 2.40 MB

english, 2007

20

Query3d: a new method for high-throughput analysis of functional residues in protein structures

Gabriele Ausiello, Allegra Via, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 225 KB

english, 2005

21

Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information

Fabrizio Ferrè, Allegra Via, Gabriele Ausiello, Barbara Brannetti, Andreas Zanzoni, Manuela Helmer-Citterich

Journal:

Comparative and Functional Genomics

Year:

2003

Language:

english

File:

PDF, 76 KB

english, 2003

22

A structural study for the optimisation of functional motifs encoded in protein sequences

Allegra Via, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Year:

2004

Language:

english

File:

PDF, 849 KB

english, 2004

23

Most yeast SH3 domains bind peptide targets with high intrinsic specificity

Brown, Tom, Brown, Nick, Stollar, Elliott J., Helmer-Citterich, Manuela

Journal:

Year:

2018

Language:

english

File:

PDF, 11.68 MB

english, 2018

24

Evolution of protein structure and function

Michael Sternberg, Syed Nabil Ali, Manuela Helmer-Citterich, Pier F. Gherardini, Keiran Fleming, Lawrence A. Kelley, Mark N. Wass

Journal:

Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology

Year:

2009

Language:

english

File:

PDF, 57 KB

english, 2009

25

Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound

Leclercq, Olivier, Bartho, Kathrin, Duelsner, Erik, von Kleist, Lisa, Gherardini, Pier Federico, Palmeri, Antonio, Helmer-Citterich, Manuela, Baumgart, Sabine, Späth, Gerald F.

Journal:

Journal of Proteomics

Year:

2013

Language:

english

File:

PDF, 800 KB

english, 2013

26

Two Structural Motifs within Canonical EF-Hand Calcium-Binding Domains Identify Five Different Classes of Calcium Buffers and Sensors

Denessiouk, Konstantin, Permyakov, Sergei, Denesyuk, Alexander, Permyakov, Eugene, Johnson, Mark S., Helmer-Citterich, Manuela

Journal:

Year:

2014

Language:

english

File:

PDF, 1.10 MB

english, 2014

27

RISC RNA sequencing in the Dorsal RaphÃ¨ reveals microRNAs regulatory activities associated with behavioral and functional adaptations to chronic stress

Babicola, Lucy, Pietrosanto, Marco, Ielpo, Donald, D'Addario, Sebastian Luca, Cabib, Simona, Ventura, Rossella, Ferlazzo, Fabio, Helmer-Citterich, Manuela, Andolina, Diego, Lo Iacono, Luisa

Journal:

Year:

2020

File:

PDF, 1.25 MB

2020

28

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures

Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 555 KB

english, 2008

29

A structure filter for the Eukaryotic Linear Motif Resource

Allegra Via, Cathryn M Gould, Christine Gemünd, Toby J Gibson, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.60 MB

english, 2009

30

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities

Valerio Bianchi, Pier Federico Gherardini, Manuela Helmer-Citterich, Gabriele Ausiello

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 598 KB

english, 2012

31

Div-BLAST: Diversification of Sequence Search Results

Eser, Elif, Can, Tolga, Ferhatosmanoğlu, Hakan, Helmer-Citterich, Manuela

Journal:

Year:

2014

Language:

english

File:

PDF, 1.12 MB

english, 2014

32

Functional annotation by identification of local surface similarities: a novel tool for structural genomics

Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.29 MB

english, 2005

33

Mapping the human phosphatome on growth pathways

Sacco, Francesca, Gherardini, Pier Federico, Paoluzi, Serena, Saez-Rodriguez, Julio, Helmer-Citterich, Manuela, Ragnini-Wilson, Antonella, Castagnoli, Luisa, Cesareni, Gianni

Journal:

Molecular Systems Biology

Year:

2012

Language:

english

File:

PDF, 722 KB

english, 2012

34

A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks

Kerkhofs, Johan, Geris, Liesbet, Helmer-Citterich, Manuela

Journal:

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

35

ANKRD54 preferentially selects Bruton’s Tyrosine Kinase (BTK) from a Human Src-Homology 3 (SH3) domain library

Gustafsson, Manuela O., Mohammad, Dara K., Ylösmäki, Erkko, Choi, Hyunseok, Shrestha, Subhash, Wang, Qing, Nore, Beston F., Saksela, Kalle, Smith, C. I. Edvard, Helmer-Citterich, Manuela

Journal:

Year:

2017

Language:

english

File:

PDF, 1.14 MB

english, 2017

36

Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics

Paolo Romano, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 112 KB

english, 2012

37

What has proteomics taught us about Leishmania development?

TSIGANKOV, POLINA, GHERARDINI, PIER FEDERICO, HELMER-CITTERICH, MANUELA, ZILBERSTEIN, DAN

Journal:

Year:

2012

Language:

english

File:

PDF, 539 KB

english, 2012

38

Analysis of Non-Typeable Haemophilous influenzae VapC1 Mutations Reveals Structural Features Required for Toxicity and Flexibility in the Active Site

Hamilton, Brooke, Manzella, Alexander, Schmidt, Karyn, DiMarco, Victoria, Butler, J. Scott, Helmer-Citterich, Manuela

Journal:

Year:

2014

Language:

english

File:

PDF, 4.18 MB

english, 2014

39

Computational Analysis of the Predicted Evolutionary Conservation of Human Phosphorylation Sites

Trost, Brett, Kusalik, Anthony, Napper, Scott, Helmer-Citterich, Manuela

Journal:

Year:

2016

Language:

english

File:

PDF, 1.86 MB

english, 2016

40

CavBench: A benchmark for protein cavity detection methods

Dias, Sérgio, Simões, Tiago, Fernandes, Francisco, Martins, Ana Mafalda, Ferreira, Alfredo, Jorge, Joaquim, Gomes, Abel J. P., Helmer-Citterich, Manuela

Journal:

Year:

2019

Language:

english

File:

PDF, 2.71 MB

english, 2019

41

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society

Manuela Helmer-Citterich, Rita Casadio, Alessandro Guffanti, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Giorgio Valle, Cecilia Saccone

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 191 KB

english, 2005

42

Phosphoproteomic Analysis of Differentiating Leishmania Parasites Reveals a Unique Stage-Specific Phosphorylation Motif

Tsigankov, Polina, Gherardini, Pier Federico, Helmer-Citterich, Manuela, Späth, Gerald F., Zilberstein, Dan

Journal:

Journal of Proteome Research

Year:

2013

Language:

english

File:

PDF, 2.65 MB

english, 2013

43

Experimental and computational methods for the analysis and modeling of signaling networks

Gherardini, Pier Federico, Helmer-Citterich, Manuela

Journal:

New Biotechnology

Year:

2013

Language:

english

File:

PDF, 189 KB

english, 2013

44

Modeling gene regulatory network motifs using statecharts

Fabio Fioravanti, Manuela Helmer-Citterich, Enrico Nardelli

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 934 KB

english, 2012

45

Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search

Alocci, Davide, Mariethoz, Julien, Horlacher, Oliver, Bolleman, Jerven T., Campbell, Matthew P., Lisacek, Frederique, Helmer-Citterich, Manuela

Journal:

Year:

2015

Language:

english

File:

PDF, 1.35 MB

english, 2015

46

Molecular Insights into the Transmembrane Domain of the Thyrotropin Receptor

Chantreau, Vanessa, Taddese, Bruck, Munier, Mathilde, Gourdin, Louis, Henrion, Daniel, Rodien, Patrice, Chabbert, Marie, Helmer-Citterich, Manuela

Journal:

Year:

2015

Language:

english

File:

PDF, 3.06 MB

english, 2015

47

Discovering sequence and structure landscapes in RNA interaction motifs

Adinolfi, Marta, Pietrosanto, Marco, Parca, Luca, Ausiello, Gabriele, Ferrè, Fabrizio, Helmer-Citterich, Manuela

Journal:

Nucleic Acids Research

Year:

2019

File:

PDF, 5.54 MB

2019

48

Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics

Rita Casadio, Manuela Helmer-Citterich, Graziano Pesole

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 172 KB

english, 2007

49

Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon

Pier Federico Gherardini, Mark N. Wass, Manuela Helmer-Citterich, Michael J.E. Sternberg

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1020 KB

english, 2007

50

Deciphering a global network of functionally associated post-translational modifications

Minguez, Pablo, Parca, Luca, Diella, Francesca, Mende, Daniel R, Kumar, Runjun, Helmer-Citterich, Manuela, Gavin, Anne-Claude, van Noort, Vera, Bork, Peer

Journal:

Molecular Systems Biology

Year:

2012

Language:

english

File:

PDF, 560 KB

english, 2012

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