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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

Comparative protein structure modeling of genes and genomes

Sali, A., Eswar, N., Pieper, U., Marti-Renom, M. A., Madhusudhan, M., Fiser, A., Ilyin, V.

Journal:

Acta Crystallographica Section A Foundations of Crystallography

Year:

2002

Language:

english

File:

PDF, 21 KB

english, 2002

6

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

7

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

8

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

9

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

10

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

11

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

12

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

13

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

14

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

15

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

16

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

17

Classification of protein disulphide-bridge topologies

J.M. Mas, P. Aloy, M.A. Martí-Renom, B. Oliva, R. de Llorens, F.X. Avilés, E. Querol

Journal:

Journal of Computer-Aided Molecular Design

Year:

2001

Language:

english

File:

PDF, 208 KB

english, 2001

18

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

19

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

20

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

21

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

22

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

23

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

24

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

25

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

26

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

27

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

28

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

29

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

30

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

31

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

32

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

33

Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package

Kemena, C., Bussotti, G., Capriotti, E., Marti-Renom, M. A., Notredame, C.

Journal:

Year:

2013

Language:

english

File:

PDF, 323 KB

english, 2013

34

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

35

Variable gap penalty for protein sequence-structure alignment

Madhusudhan, M.S., Marti-Renom, M. A., Sanchez, R., Sali, A.

Journal:

Protein Engineering Design and Selection

Year:

2006

Language:

english

File:

PDF, 192 KB

english, 2006

36

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

37

Detecting remotely related proteins by their interactions and sequence similarity

Espadaler, J., Aragues, R., Eswar, N., Marti-Renom, M. A., Querol, E., Aviles, F. X., Sali, A., Oliva, B.

Journal:

Proceedings of the National Academy of Sciences

Year:

2005

Language:

english

File:

PDF, 699 KB

english, 2005

38

SARA: a server for function annotation of RNA structures

Capriotti, E., Marti-Renom, M. A.

Journal:

Nucleic Acids Research

Year:

2009

Language:

english

File:

PDF, 1.94 MB

english, 2009

39

A Novel Family of Soluble Minimal Scaffolds Provides Structural Insight into the Catalytic Domains of Integral Membrane Metallopeptidases

Lopez-Pelegrin, M., Cerda-Costa, N., Martinez-Jimenez, F., Cintas-Pedrola, A., Canals, A., Peinado, J. R., Marti-Renom, M. A., Lopez-Otin, C., Arolas, J. L., Gomis-Ruth, F. X.

Journal:

Journal of Biological Chemistry

Year:

2013

Language:

english

File:

PDF, 4.61 MB

english, 2013

40

DBAli tools: mining the protein structure space

Marti-Renom, M. A., Pieper, U., Madhusudhan, M. S., Rossi, A., Eswar, N., Davis, F. P., Al-Shahrour, F., Dopazo, J., Sali, A.

Journal:

Nucleic Acids Research

Year:

2007

Language:

english

File:

PDF, 4.91 MB

english, 2007

41

Impact of fgd1 and ddn Diversity in Mycobacterium tuberculosis Complex on In Vitro Susceptibility to PA-824

Feuerriegel, S., Koser, C. U., Bau, D., Rusch-Gerdes, S., Summers, D. K., Archer, J. A. C., Marti-Renom, M. A., Niemann, S.

Journal:

Antimicrobial Agents and Chemotherapy

Year:

2011

Language:

english

File:

PDF, 70 KB

english, 2011

42

DBAli: a database of protein structure alignments

Marti-Renom, M. A., Ilyin, V. A., Sali, A.

Journal:

Year:

2001

Language:

english

File:

PDF, 103 KB

english, 2001

43

EVA: continuous automatic evaluation of protein structure prediction servers

Eyrich, V. A., Marti-Renom, M. A., Przybylski, D., Madhusudhan, M. S., Fiser, A., Pazos, F., Valencia, A., Sali, A., Rost, B.

Journal:

Year:

2001

Language:

english

File:

PDF, 68 KB

english, 2001

44

Use of Single Point Mutations in Domain I of 2-Glycoprotein I to Determine Fine Antigenic Specificity of Antiphospholipid Autoantibodies

Iverson, G. M., Reddel, S., Victoria, E. J., Cockerill, K. A., Wang, Y.-X., Marti-Renom, M. A., Sali, A., Marquis, D. M., Krilis, S. A., Linnik, M. D.

Journal:

The Journal of Immunology

Year:

2002

Language:

english

File:

PDF, 819 KB

english, 2002

45

All-atom knowledge-based potential for RNA structure prediction and assessment

Capriotti, E., Norambuena, T., Marti-Renom, M. A., Melo, F.

Journal:

Year:

2011

Language:

english

File:

PDF, 288 KB

english, 2011

46

RNA structure alignment by a unit-vector approach

Capriotti, E., Marti-Renom, M. A.

Journal:

Year:

2008

Language:

english

File:

PDF, 1016 KB

english, 2008

47

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

48

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

49

ModView, visualization of multiple protein sequences and structures

Ilyin, V. A., Pieper, U., Stuart, A. C., Marti-Renom, M. A., McMahan, L., Sali, A.

Journal:

Year:

2003

Language:

english

File:

PDF, 317 KB

english, 2003

50

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