ASAP: analysis of peptide composition. - Xavier Serra-Hartmann; Xavier Rebordosa; Jaume Piñol; Enrique Querol; Marc A. Martí-Renom (Bioinform., 2000)

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 (J. Comput. Aided Mol. Des., 2000)

EVA: continuous automatic evaluation of protein structure prediction servers. - Volker A. Eyrich; Marc A. Martí-Renom; Dariusz Przybylski; Mallur S. Madhusudhan; András Fiser; Florencio Pazos; Alfonso Valencia; Andrej Sali; Burkhard Rost (Bioinform., 2001)

DBAli: a database of protein structure alignments. - Marc A. Martí-Renom; Valentin A. Ilyin; Andrej Sali (Bioinform., 2001)

Classification of protein disulphide-bridge topologies. - José M. Mas; Patrick Aloy; Marc A. Martí-Renom; Baldomero Oliva; R. de Llorens; Francesc X. Avilés; Enrique Querol (J. Comput. Aided Mol. Des., 2001)

ModView, visualization of multiple protein sequences and structures. - Valentin A. Ilyin; Ursula Pieper 001; Ashley C. Stuart; Marc A. Martí-Renom; Linda McMahan; Andrej Sali (Bioinform., 2003)

Tools for comparative protein structure modeling and analysis. - Narayanan Eswar; Bino John; Nebojsa Mirkovic; András Fiser; Valentin A. Ilyin; Ursula Pieper 001; Ashley C. Stuart; Marc A. Martí-Renom; Mallur S. Madhusudhan; Bozidar Yerkovich; Andrej Sali (Nucleic Acids Res., 2003)

EVA: evaluation of protein structure prediction servers. - Ingrid Y. Y. Koh; Volker A. Eyrich; Marc A. Martí-Renom; Dariusz Przybylski; Mallur S. Madhusudhan; Narayanan Eswar; Osvaldo Graña; Florencio Pazos; Alfonso Valencia; Andrej Sali; Burkhard Rost (Nucleic Acids Res., 2003)

MODBASE, a database of annotated comparative protein structure models, and associated resources. - Ursula Pieper 001; Narayanan Eswar; Hannes Braberg; Mallur S. Madhusudhan; Fred P. Davis; Ashley C. Stuart; Nebojsa Mirkovic; Andrea Rossi 005; Marc A. Martí-Renom; András Fiser; Ben M. Webb; Daniel M. Greenblatt; et al. (Nucleic Acids Res., 2004)

MODBASE: a database of annotated comparative protein structure models and associated resources. - Ursula Pieper 001; Narayanan Eswar; Fred P. Davis; Hannes Braberg; Mallur S. Madhusudhan; Andrea Rossi 005; Marc A. Martí-Renom; Rachel Karchin; Ben M. Webb; David Eramian; Min-Yi Shen; Libusha Kelly; et al. (Nucleic Acids Res., 2006)

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. - Marc A. Martí-Renom; Andrea Rossi 005; Fátima Al-Shahrour; Fred P. Davis; Ursula Pieper 001; Joaquín Dopazo; Andrej Sali (BMC Bioinform., 2007)

DBAli tools: mining the protein structure space. - Marc A. Martí-Renom; Ursula Pieper 001; Mallur S. Madhusudhan; Andrea Rossi 005; Narayanan Eswar; Fred P. Davis; Fátima Al-Shahrour; Joaquín Dopazo; Andrej Sali (Nucleic Acids Res., 2007)

Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions. - Ramon Aragues; Andrej Sali; Jaume Bonet; Marc A. Martí-Renom; Baldo Oliva (PLoS Comput. Biol., 2007)

RNA structure alignment by a unit-vector approach. - Emidio Capriotti; Marc A. Martí-Renom (ECCB, 2008)

Prediction of enzyme function by combining sequence similarity and protein interactions. - Jordi Espadaler; Narayanan Eswar; Enrique Querol; Francesc X. Avilés; Andrej Sali; Marc A. Martí-Renom; Baldomero Oliva (BMC Bioinform., 2008)

ModLink+: improving fold recognition by using protein-protein interactions. - Oriol Fornes; Ramon Aragues; Jordi Espadaler; Marc A. Martí-Renom; Andrej Sali; Baldo Oliva (Bioinform., 2009)

SARA: a server for function annotation of RNA structures. - Emidio Capriotti; Marc A. Martí-Renom (Nucleic Acids Res., 2009)

MODBASE, a database of annotated comparative protein structure models and associated resources. - Ursula Pieper 001; Narayanan Eswar; Ben M. Webb; David Eramian; Libusha Kelly; David T. Barkan; Hannah Carter; Parminder Mankoo; Rachel Karchin; Marc A. Martí-Renom; Fred P. Davis; Andrej Sali (Nucleic Acids Res., 2009)

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. - Emidio Capriotti; Marc A. Martí-Renom (BMC Bioinform., 2010)

All-atom knowledge-based potential for RNA structure prediction and assessment. - Emidio Capriotti; Tomás Norambuena; Marc A. Martí-Renom; Francisco Melo 001 (Bioinform., 2011)

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization. - Marc A. Martí-Renom; Leonid A. Mirny (PLoS Comput. Biol., 2011)

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation. - Marc A. Martí-Renom (RECOMB, 2012)

Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package. - Carsten Kemena; Giovanni Bussotti; Emidio Capriotti; Marc A. Martí-Renom; Cédric Notredame (Bioinform., 2013)

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis. - Francisco Martínez-Jiménez; George Papadatos; Lun Yang; Iain M. Wallace; Vinod Kumar; Ursula Pieper 001; Andrej Sali; James R. Brown; John P. Overington; Marc A. Martí-Renom (PLoS Comput. Biol., 2013)

Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze. - Francisco Martínez-Jiménez; Marc A. Martí-Renom (PLoS Comput. Biol., 2015)

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors. - François Serra; Davide Baù; Mike Goodstadt; David Castillo; Guillaume J. Filion; Marc A. Martí-Renom (PLoS Comput. Biol., 2017)