CyToStruct: augmenting the network visualization of cytoscape with the power of molecular viewers

VMD: visual molecular dynamics

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The PyMOL Molecular Graphics System

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Inference of macromolecular assemblies from crystalline state.

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Electrostatics of nanosystems: Application to microtubules and the ribosome

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The Large-Scale Organization of Metabolic Networks

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Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

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Ligand docking and binding site analysis with PyMOL and Autodock/Vina

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Relating protein pharmacology by ligand chemistry

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A travel guide to Cytoscape plugins

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A discussion of the solution for the best rotation to relate two sets of vectors

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SCOP: a Structural Classification of Proteins database

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Structure-based prediction of protein–protein interactions on a genome-wide scale

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Global alignment of multiple protein interaction networks with application to functional orthology detection

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Computer-aided drug design platform using PyMOL

Lill, M. A., & Danielson, M. L. (2010) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-010-9395-8 · Cited by 648 · see citing works

Protein structure prediction from sequence variation

Marks, D. S., Hopf, T. A., & Sander, C. (2012) · Nature Biotechnology · doi:10.1038/nbt.2419 · Cited by 622 · see citing works

Emerging methods in protein co-evolution

de Juan, D., Pazos, F., & Valencia, A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3414 · Cited by 607 · see citing works

Network Analysis of Protein Structures Identifies Functional Residues

Amitai, G., Shemesh, A., Sitbon, E., Shklar, M., Netanely, D., Venger, I., & Pietrokovski, S. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.10.055 · Cited by 504 · see citing works

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

Lasker, K., Förster, F. G., Bohn, S., Walzthoeni, T., Villa, E., Unverdorben, P., Beck, F., Aebersold, R. H., Šali, A., & Baumeister, W. P. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120559109 · Cited by 442 · see citing works

CATH: comprehensive structural and functional annotations for genome sequences

Sillitoe, I., Lewis, T. E., Cuff, A. L., Das, S., Ashford, P., Dawson, N. L., Furnham, N., Laskowski, R. A., Lee, D., Lees, J. G., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku947 · Cited by 424 · see citing works

Structure-Based Assembly of Protein Complexes in Yeast

Aloy, P., Böttcher, B., Ceulemans, H., Leutwein, C., Mellwig, C., Fischer, S., Gavin, A.-C., Bork, P., Superti-Furga, G., Serrano, L., et al. (2004) · Science · doi:10.1126/science.1092645 · Cited by 383 · see citing works

Interrogating protein interaction networks through structural biology

Aloy, P., & Russell, R. B. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.092147999 · Cited by 342 · see citing works

Structural systems biology: modelling protein interactions

Aloy, P., & Russell, R. B. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1859 · Cited by 327 · see citing works

Structure of the large ribosomal subunit from human mitochondria

Brown, A., Amunts, A., Bai, X., Sugimoto, Y., Edwards, P. C., Murshudov, G. N., Scheres, S. H. W., & Ramakrishnan, V. (2014) · Science · doi:10.1126/science.1258026 · Cited by 324 · see citing works

COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes

Vangone, A., Spinelli, R., Scarano, V., Cavallo, L., & Oliva, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr484 · Cited by 263 · see citing works

Analyzing and visualizing residue networks of protein structures

Doncheva, N. T., Klein, K., Domingues, F. S., & Albrecht, M. (2011) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.01.002 · Cited by 259 · see citing works

NetworkView: 3D display and analysis of protein·RNA interaction networks

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Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

Zhang, Y., Thiele, I., Weekes, D., Li, Z., Jaroszewski, L., Ginalski, K., Deacon, A. M., Wooley, J., Lesley, S. A., Wilson, I. A., et al. (2009) · Science · doi:10.1126/science.1174671 · Cited by 188 · see citing works

Expanding protein universe and its origin from the biological Big Bang

Dokholyan, N. V., Shakhnovich, B. E., & Shakhnovich, E. I. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202497999 · Cited by 176 · see citing works

Visualization of macromolecular structures

O’Donoghue, S. I., Goodsell, D. S., Frangakis, A. S., Jossinet, F., Laskowski, R. A., Nilges, M., Saibil, H. R., Schafferhans, A., Wade, R. C., Westhof, É., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1427 · Cited by 167 · see citing works

The evolution of domain arrangements in proteins and interaction networks

Bornberg‐Bauer, E., Beaussart, F., Kummerfeld, S., Teichmann, S. A., & Weiner, J. M. (2005) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-004-4416-1 · Cited by 124 · see citing works

Widespread Head-to-Head Hydrocarbon Biosynthesis in Bacteria and Role of OleA

Sukovich, D. J., Seffernick, J. L., Richman, J. E., Gralnick, J. A., & Wackett, L. P. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00436-10 · Cited by 122 · see citing works

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

Chang, R. L., Andrews, K. A., Kim, D., Li, Z., Godzik, A., & Palsson, B. Ø. (2013) · Science · doi:10.1126/science.1234012 · Cited by 116 · see citing works

PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins

Tiberti, M., Invernizzi, G., Lambrughi, M., Inbar, Y., Schreiber, G., & Papaleo, E. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci400639r · Cited by 100 · see citing works

Targeting and tinkering with interaction networks

Russell, R. B., & Aloy, P. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.119 · Cited by 99 · see citing works

Three-dimensional modeling of protein interactions and complexes is going ‘omics

Stein, A., Mosca, R., & Aloy, P. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.01.005 · Cited by 94 · see citing works

A galaxy of folds

Alva, V., Remmert, M., Biegert, A., Lupas, A. N., & Söding, J. (2009) · Protein Science · doi:10.1002/pro.297 · Cited by 83 · see citing works

The continuity of protein structure space is an intrinsic property of proteins

Skolnick, J., Arakaki, A. K., Lee, S. Y., & Bryliński, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907683106 · Cited by 83 · see citing works

structureViz: linking cytoscape and UCSF Chimera

Morris, J. H., Huang, C. C., Babbitt, P. C., & Ferrin, T. E. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm329 · Cited by 82 · see citing works

Global view of the protein universe

Nepomnyachiy, S., Ben‐Tal, N., & Kolodny, R. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1403395111 · Cited by 80 · see citing works

xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures.

Pasi, M., Tiberti, M., Arrigoni, A., & Papaleo, E. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300213c · Cited by 80 · see citing works

Evolutionary relationship of two ancient protein superfolds

Farías‐Rico, J. A., Schmidt, S., & Höcker, B. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1579 · Cited by 75 · see citing works

Integrative structure modeling of macromolecular assemblies from proteomics data

Lasker, K., Phillips, J. L., Russel, D., Velázquez-Muriel, J., Schneidman-Duhovny, D., Tjioe, E., Webb, B., Schlessinger, A., & Sali, A. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r110.000067 · Cited by 71 · see citing works

Protein structure networks

Greene, L. H. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/els039 · Cited by 62 · see citing works

Structural Bioinformatics of the Interactome

Petrey, D. S., & Honig, B. H. (2014) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-051013-022726 · Cited by 59 · see citing works

Investigative mining of sequence data for novel enzymes: A case study with nitrilases

Seffernick, J. L., Samanta, S. K., Louie, T. M., Wackett, L. P., & Subramanian, M. V. (2009) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2009.06.004 · Cited by 51 · see citing works

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets

Hosur, R., Peng, J., Vinayagam, A., Stelzl, U., Xu, J., Perrimon, N., Bienkowska, J. R., & Berger, B. (2012) · Genome biology · doi:10.1186/gb-2012-13-8-r76 · Cited by 46 · see citing works

PyDeT, a PyMOL plug-in for visualizing geometric concepts around proteins

Ördög, R. (2008) · Bioinformation · doi:10.6026/97320630002346 · Cited by 41 · see citing works

SPEER-SERVER: a web server for prediction of protein specificity determining sites

Chakraborty, A., Mandloi, S., Lanczycki, C. J., Panchenko, A. R., & Chakrabarti, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks559 · Cited by 32 · see citing works

DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks

Xiong, B., Liu, K., Wu, J., Burk, D. L., Jiang, H., & Shen, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn389 · Cited by 16 · see citing works

N-terminal region of human chemokine receptor CXCR3: Structural analysis of CXCR3(1–48) by experimental and computational studies

Raucci, R., Colonna, G., Giovane, A., Castello, G., & Costantini, S. (2014) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2014.08.004 · Cited by 11 · see citing works

Representation of the Protein Universe using Classifications, Maps, and Networks

Ben‐Tal, N., & Kolodny, R. (2014) · Israel Journal of Chemistry · doi:10.1002/ijch.201400001 · Cited by 11 · see citing works

Graphlet signature-based scoring method to estimate protein–ligand binding affinity

Singh, O., Sawariya, K., & Aparoy, P. (2014) · Royal Society Open Science · doi:10.1098/rsos.140306 · Cited by 9 · see citing works

Predicting Protein–Protein Interactions from the Molecular to the Proteome Level

Keskin, O., Tuncbag, N., & Gursoy, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00683 · Cited by 369 · see citing works

NAPS: Network Analysis of Protein Structures

Chakrabarty, B., & Parekh, N. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw383 · Cited by 174 · see citing works

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass

Viloria, J. S., Allega, M. F., Lambrughi, M., & Papaleo, E. (2017) · Scientific Reports · doi:10.1038/s41598-017-01498-6 · Cited by 109 · see citing works

Mapping the multiscale structure of biological systems

Schaffer, L. V., & Ideker, T. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.012 · Cited by 75 · see citing works

Bridging Themes: Short Protein Segments Found in Different Architectures

Kolodny, R., Nepomnyachiy, S., Tawfik, D. S., & Ben‐Tal, N. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab017 · Cited by 63 · see citing works

NAPS update: network analysis of molecular dynamics data and protein–nucleic acid complexes

Chakrabarty, B., Naganathan, V., GARG, K., Agarwal, Y., & Parekh, N. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz399 · Cited by 56 · see citing works

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

Franklin, M. W., Nepomnyachiy, S., Feehan, R., Ben‐Tal, N., Kolodny, R., & Slusky, J. S. G. (2018) · eLife · doi:10.7554/elife.40308 · Cited by 33 · see citing works

Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold

Franklin, M. W., Nepomnyachiy, S., Feehan, R., Ben‐Tal, N., Kolodny, R., & Slusky, J. S. G. (2018) · Structure · doi:10.1016/j.str.2018.06.007 · Cited by 24 · see citing works

Similar protein segments shared between domains of different evolutionary lineages

Qiu, K., Ben‐Tal, N., & Kolodny, R. (2022) · Protein Science · doi:10.1002/pro.4407 · Cited by 23 · see citing works

XlinkCyNET: A Cytoscape Application for Visualization of Protein Interaction Networks Based on Cross-Linking Mass Spectrometry Identifications

Lima, D. B., Zhu, Y., & Liu, F. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00957 · Cited by 22 · see citing works

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

Narunsky, A., Nepomnyachiy, S., Ashkenazy, H., Kolodny, R., & Ben‐Tal, N. (2015) · Structure · doi:10.1016/j.str.2015.08.018 · Cited by 14 · see citing works

ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes

Razban, R. M., Gilson, A. I., Durfee, N., Strobelt, H., Dinkla, K., Choi, J., Pfister, H., & Shakhnovich, E. I. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty370 · Cited by 5 · see citing works

AQcalc : A web server that identifies weak molecular interactions in protein structures

Afshinpour, M., Smith, L. A., & Chakravarty, S. (2023) · Protein Science · doi:10.1002/pro.4762 · Cited by 3 · see citing works

Navigating Among Known Structures in Protein Space

Narunsky, A., Ben‐Tal, N., & Kolodny, R. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8736-8_12 · Cited by 3 · see citing works

JSONWP: a static website generator for protein bioinformatics research

Kilinc, M., Jia, K., & Jernigan, R. L. (2023) · Bioinformatics Advances · doi:10.1093/bioadv/vbad154 · Cited by 1 · see citing works

CyToServer -- A developer tool to bridge between network and 3D-structure

Nepomnyachiy, S., Ben‐Tal, N., & Kolodny, R. (2015) · doi:10.7490/f1000research.1110155.1

Evolution of Environmentally-Enforced, Repeat Protein Topology in the Outer MembranePreprint

Franklin, M. W., Nepomnyachiy, S., Feehan, R., Ben‐Tal, N., Kolodny, R., & Slusky, J. S. G. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/309393

Labeling and visual attributes

Hansen, D. L., Shneiderman, B., Smith, M. A., & Himelboim, I. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-817756-3.00005-4

Faculty Opinions recommendation of Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold.

Casadio, R. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733716805.793549003

Structural conservation and divergence across the Receptor Tyrosine Kinase superfamilyPreprint

Bakhman, A. F., Kolodny, R., & Kosloff, M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.31.630944

ComplexViewer: visualization of curated macromolecular complexes

Combe, C., Sivade, M., Hermjakob, H., Heimbach, J., Meldal, B., Micklem, G., Orchard, S. E., & Rappsilber, J. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx497 · Cited by 16 · see citing works

BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm329 Systems biology structureViz: linking Cytoscape and UCSF Chimera

Morris, J. H., Huang, C. C., Babbitt, P. C., & Ferrin, T. E. (2008)

structureViz: linking cytoscape and UCSF Chimera

Morris, J. H., Huang, C. C., Babbitt, P. C., & Ferrin, T. E. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm329 · Cited by 82 · see citing works

Biomolecular network visualization based on CPSE-Bio

Xie, J., -, Y. R., Zhang, H., Wu, Z., & Kawata, S. (2012) · International Conference on Computing and Convergence Technology · Cited by 2 · see citing works

Web application for visualizing molecular interaction networks based on cytoscape.js

Lysenko, K. (2024) · RepositóriUM (Universidade do Minho)