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1

Prediction of enzyme function by combining sequence similarity and protein interactions

Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X Avilés, Andrej Sali, Marc A Marti-Renom, Baldomero Oliva

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 958 KB

english, 2008

2

COMPARATIVE PROTEIN STRUCTURE MODELING OF GENES AND GENOMES

Martí-Renom, Marc A., Stuart, Ashley C., Fiser, András, Sánchez, Roberto, Melo, Francisco, Šali, Andrej

Journal:

Annual Review of Biophysics and Biomolecular Structure

Year:

2000

Language:

english

File:

PDF, 352 KB

english, 2000

3

Structure-based statistical analysis of transmembrane helices

Carlos Baeza-Delgado, Marc A. Marti-Renom, Ismael Mingarro

Journal:

European Biophysics Journal

Year:

2013

Language:

english

File:

PDF, 615 KB

english, 2013

4

Software for predicting the 3D structure of RNA molecules

Dufour, David, Marti-Renom, Marc A.

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2015

Language:

english

File:

PDF, 182 KB

english, 2015

5

Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints

Marc A. Martí-Renom, Roland H. Stote, Enrique Querol, Francesc X. Aviles, Martin Karplus

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 174 KB

english, 2000

6

Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans

Emidio Capriotti, Leonardo Arbiza, Rita Casadio, Joaquín Dopazo, Hernán Dopazo, Marc A. Marti-Renom

Journal:

Year:

2008

Language:

english

File:

PDF, 238 KB

english, 2008

7

N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon

Manuel Bañó-Polo, Francesca Baldin, Silvia Tamborero, Marc A. Marti-Renom, Ismael Mingarro

Journal:

Protein Science

Year:

2011

Language:

english

File:

PDF, 700 KB

english, 2011

8

Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets

Francisco Melo, Marc A. Marti-Renom

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 205 KB

english, 2006

9

Statistical Analysis of the Loop-Geometry on a Non-Redundant Database of Proteins

Marc A. Martí-Renom, José M. Mas, Patrick Aloy, Enrique Querol, Francesc X. Avilés, Baldomero Oliva

Journal:

Journal of Molecular Modeling

Year:

1998

Language:

english

File:

PDF, 197 KB

english, 1998

10

Structure determination of genomic domains by satisfaction of spatial restraints

Davide Baù, Marc A. Marti-Renom

Journal:

Chromosome Research

Year:

2011

Language:

english

File:

PDF, 417 KB

english, 2011

11

Membrane protein integration into the endoplasmic reticulum

Luis Martínez-Gil, Ana Saurí, Marc A. Marti-Renom, Ismael Mingarro

Journal:

Year:

2011

Language:

english

File:

PDF, 277 KB

english, 2011

12

10.1038/80776

Sánchez, Roberto, Pieper, Ursula, Melo, Francisco, Eswar, Narayanan, Martí-Renom, Marc A., Madhusudhan, M.S., Mirković, Nebojša, Šali, Andrej

Journal:

Natural Structural Biology

Year:

2000

Language:

english

File:

PDF, 209 KB

english, 2000

13

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

Baù, Davide, Sanyal, Amartya, Lajoie, Bryan R, Capriotti, Emidio, Byron, Meg, Lawrence, Jeanne B, Dekker, Job, Marti-Renom, Marc A

Journal:

Nature Structural and Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.95 MB

english, 2010

14

The C-type lectin fold as an evolutionary solution for massive sequence variation

McMahon, Stephen A, Miller, Jason L, Lawton, Jeffrey A, Kerkow, Donald E, Hodes, Asher, Marti-Renom, Marc A, Doulatov, Sergei, Narayanan, Eswar, Sali, Andrej, Miller, Jeff F

Journal:

Nature Structural and Molecular Biology

Year:

2005

Language:

english

File:

PDF, 748 KB

english, 2005

15

Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2

Patrick Aloy, José M. Mas, Marc A. Martí-Renom, Enrique Querol, Francesc X. Avilés, Baldomero Oliva

Journal:

Journal of Computer-Aided Molecular Design

Year:

2000

Language:

english

File:

PDF, 178 KB

english, 2000

16

Alignment of protein sequences by their profiles

Marc A. Marti-Renom, M.S. Madhusudhan, Andrej Sali

Journal:

Protein Science

Year:

2004

Language:

english

File:

PDF, 595 KB

english, 2004

17

A composite score for predicting errors in protein structure models

David Eramian, Min-yi Shen, Damien Devos, Francisco Melo, Andrej Sali, Marc A. Marti-Renom

Journal:

Protein Science

Year:

2006

Language:

english

File:

PDF, 603 KB

english, 2006

18

Localization of binding sites in protein structures by optimization of a composite scoring function

Andrea Rossi, Marc A. Marti-Renom, Andrej Sali

Journal:

Protein Science

Year:

2006

Language:

english

File:

PDF, 747 KB

english, 2006

19

Chromatin globules: a common motif of higher order chromosome structure?

Amartya Sanyal, Davide Baù, Marc A Martí-Renom, Job Dekker

Journal:

Current Opinion in Cell Biology

Year:

2011

Language:

english

File:

PDF, 860 KB

english, 2011

20

Reply to Moult et al.

Andrej Sali, Marc A Marti-Renom, M.S Madhusudhan, András Fiser, Burkhard Rost

Journal:

Year:

2002

Language:

english

File:

PDF, 28 KB

english, 2002

21

Reliability of Assessment of Protein Structure Prediction Methods

Marc A Marti-Renom, M.S Madhusudhan, András Fiser, Burkhard Rost, Andrej Sali

Journal:

Year:

2002

Language:

english

File:

PDF, 335 KB

english, 2002

22

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA

Emidio Capriotti, Marc A Marti-Renom

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.88 MB

english, 2010

23

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

Marc A Marti-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 644 KB

english, 2007

24

Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting

Maya Topf, Matthew L. Baker, Marc A. Marti-Renom, Wah Chiu, Andrej Sali

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 717 KB

english, 2006

25

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

Mark A. Umbarger, Esteban Toro, Matthew A. Wright, Gregory J. Porreca, Davide Baù, Sun-Hae Hong, Michael J. Fero, Lihua J. Zhu, Marc A. Marti-Renom, Harley H. McAdams, Lucy Shapiro, Job Dekker, George

Journal:

Year:

2011

Language:

english

File:

PDF, 3.89 MB

english, 2011

26

Vanilloid Receptor–Related Osmotically Activated Channel (VR-OAC), a Candidate Vertebrate Osmoreceptor

Wolfgang Liedtke, Yong Choe, Marc A. Martí-Renom, Andrea M. Bell, Charlotte S. Denis, AndrejŠali, A.J. Hudspeth, Jeffrey M. Friedman, Stefan Heller

Journal:

Year:

2000

Language:

english

File:

PDF, 1.77 MB

english, 2000

27

Protein translocation into peroxisomes by ring-shaped import receptors

Will A. Stanley, Krisztian Fodor, Marc A. Marti-Renom, Wolfgang Schliebs, Matthias Wilmanns

Journal:

Year:

2007

Language:

english

File:

PDF, 614 KB

english, 2007

28

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

Davide Baù, Marc A. Marti-Renom

Journal:

Year:

2012

Language:

english

File:

PDF, 991 KB

english, 2012

29

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

Dekker, Job, Marti-Renom, Marc A., Mirny, Leonid A.

Journal:

Nature Reviews Genetics

Year:

2013

Language:

english

File:

PDF, 6.32 MB

english, 2013

30

Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs

Alejandro Panjkovich, Francisco Melo, Marc A Marti-Renom

Journal:

Year:

2008

Language:

english

File:

PDF, 651 KB

english, 2008

31

Whole-Genome Sequencing for Rapid Susceptibility Testing of M. tuberculosis

Köser, Claudio U., Bryant, Josephine M., Becq, Jennifer, Török, M. Estée, Ellington, Matthew J., Marti-Renom, Marc A., Carmichael, Andrew J., Parkhill, Julian, Smith, Geoffrey P., Peacock, Sharon J.

Journal:

Boston Medical and Surgical Journal

Year:

2013

Language:

english

File:

PDF, 425 KB

english, 2013

32

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

Le Dily, François, Baù, Davide, Pohl, Andy, Vicent, Guillermo P., Serra, François, Soronellas, Daniel, Castellano, Giancarlo, Wright, Roni H.G., Ballare, Cecilia, Filion, Guillaume, Marti-Renom, Marc

Journal:

Genes & Development

Year:

2014

Language:

english

File:

PDF, 7.88 MB

english, 2014

33

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis

MartÃnez-JimÃ©nez, Francisco, Papadatos, George, Yang, Lun, Wallace, Iain M., Kumar, Vinod, Pieper, Ursula, Sali, Andrej, Brown, James R., Overington, John P., Marti-Renom, Marc A., MacKerell, Alexan

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 4.55 MB

english, 2013

34

On the demultiplexing of chromosome capture conformation data

Junier, Ivan, Spill, Yannick G., Marti-Renom, Marc A., Beato, Miguel, le Dily, François

Journal:

Year:

2015

Language:

english

File:

PDF, 1.29 MB

english, 2015

35

Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner

Warnecke, Tobias, Supek, Fran, Lehner, Ben, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 625 KB

english, 2012

36

Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling

Tark-Dame, Mariliis, Jerabek, Hansjoerg, Manders, Erik M. M., Heermann, Dieter W., van Driel, Roel, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.20 MB

english, 2014

37

Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze

Martínez-Jiménez, Francisco, Marti-Renom, Marc A., Schlessinger, Avner

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.75 MB

english, 2015

38

Restraint-based three-dimensional modeling of genomes and genomic domains

Serra, François, Di Stefano, Marco, Spill, Yannick G., Cuartero, Yasmina, Goodstadt, Michael, Baù, Davide, Marti-Renom, Marc A.

Journal:

Year:

2015

Language:

english

File:

PDF, 639 KB

english, 2015

39

Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells

Sasai, Masaki, Kawabata, Yudai, Makishi, Koh, Itoh, Kazuhito, Terada, Tomoki P., Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.93 MB

english, 2013

40

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

Marti-Renom, Marc A., Mirny, Leonid A., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 630 KB

english, 2011

41

Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach

Small, Meagan C., Lopes, Pedro, Andrade, Rodrigo B., MacKerell, Alexander D., Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.85 MB

english, 2013

42

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints

Diament, Alon, Tuller, Tamir, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.04 MB

english, 2015

43

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

Doyle, Boryana, Fudenberg, Geoffrey, Imakaev, Maxim, Mirny, Leonid A., Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.07 MB

english, 2014

44

Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions

Aragues, Ramon, Sali, Andrej, Bonet, Jaume, Marti-Renom, Marc A., Oliva, Baldo

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 459 KB

english, 2007

45

Partially Glycosylated Dendrimers Block MD-2 and Prevent TLR4-MD-2-LPS Complex Mediated Cytokine Responses

Barata, Teresa S., Teo, Ian, Brocchini, Steve, Zloh, Mire, Shaunak, Sunil, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.20 MB

english, 2011

46

A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly

Burton, Brittany, Zimmermann, Michael T., Jernigan, Robert L., Wang, Yongmei, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.77 MB

english, 2012

47

Role of Histone Tails in Structural Stability of the Nucleosome

Biswas, Mithun, Voltz, Karine, Smith, Jeremy C., Langowski, Jörg, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.64 MB

english, 2011

48

A Kernel for Open Source Drug Discovery in Tropical Diseases

Ortí, Leticia, Carbajo, Rodrigo J., Pieper, Ursula, Eswar, Narayanan, Maurer, Stephen M., Rai, Arti K., Taylor, Ginger, Todd, Matthew H., Pineda-Lucena, Antonio, Sali, Andrej, Marti-Renom, Marc A., Ge

Journal:

PLoS Neglected Tropical Diseases

Year:

2009

Language:

english

File:

PDF, 1.31 MB

english, 2009

49

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

Bogu, Gireesh K., Vizán, Pedro, Stanton, Lawrence W., Beato, Miguel, Di Croce, Luciano, Marti-Renom, Marc A.

Journal:

Molecular and Cellular Biology

Year:

2015

Language:

english

File:

PDF, 2.23 MB

english, 2015

50

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer

Belton, Jon-Matthew, Lajoie, Bryan R., Audibert, Sylvain, Cantaloube, Sylvain, Lassadi, Imen, Goiffon, Isabelle, Baù, Davide, Marti-Renom, Marc A., Bystricky, Kerstin, Dekker, Job

Journal:

Year:

2015

Language:

english

File:

PDF, 4.46 MB

english, 2015