structureViz: linking cytoscape and UCSF Chimera

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works

UCSF Chimera—A visualization system for exploratory research and analysis

Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,260 · see citing works

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works

Pfam: clans, web tools and services

FINN, R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj149 · Cited by 2,307 · see citing works

ModBase, a database of annotated comparative protein structure models, and associated resources

Pieper, U., Webb, B., Barkan, D. T., Schneidman‐Duhovny, D., Schlessinger, A., Braberg, H., Yang, Z., Meng, E., Pettersen, E. F., Huang, C. C., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1091 · Cited by 1,069 · see citing works

Tools for integrated sequence-structure analysis with UCSF Chimera

Meng, E. C., Pettersen, E. F., Couch, G. S., Huang, C. C., & Ferrin, T. E. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-339 · Cited by 736 · see citing works

MODBASE: a database of annotated comparative protein structure models and associated resources

Pieper, U. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj059 · Cited by 253 · see citing works

Leveraging Enzyme Structure−Function Relationships for Functional Inference and Experimental Design: The Structure−Function Linkage Database

Pegg, S. C. ‐., Brown, S. D., Ojha, S., Seffernick, J. L., Meng, E. C., Morris, J. H., Chang, P. J., Huang, C. C., Ferrin, T. E., & Babbitt, P. C. (2006) · Biochemistry · doi:10.1021/bi052101l · Cited by 152 · see citing works

Biochemical Characterization and Crystallographic Structure of an Escherichia coli Protein from the Phosphotriesterase Gene Family

Buchbinder, J. L., Stephenson, R. C., Dresser, M. J., Pitera, J. W., Scanlan, T. S., & Fletterick, R. J. (1998) · Biochemistry · doi:10.1021/bi971707+ · Cited by 65 · see citing works

A travel guide to Cytoscape plugins

Saito, R., Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P., Lotia, S., Pico, A. R., Bader, G. D., & Ideker, T. (2012) · Nature Methods · doi:10.1038/nmeth.2212 · Cited by 1,496 · see citing works

Biological Network Exploration with Cytoscape 3

Su, G., Morris, J. H., Demchak, B., & Bader, G. D. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0813s47 · Cited by 1,037 · see citing works

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

Csermely, P., Korcsmáros, T., Kiss, H., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 889 · see citing works

UCSF Chimera, MODELLER, and IMP: An integrated modeling system

Yang, Z. R., Lasker, K., Schneidman‐Duhovny, D., Webb, B., Huang, C. C., Pettersen, E. F., Goddard, T. D., Meng, E. C., Šali, A., & Ferrin, T. E. (2011) · Journal of Structural Biology · doi:10.1016/j.jsb.2011.09.006 · Cited by 637 · see citing works

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

Atkinson, H. J., Morris, J. H., Ferrin, T. E., & Babbitt, P. C. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004345 · Cited by 459 · see citing works

The RING 2.0 web server for high quality residue interaction networks

Piovesan, D., Minervini, G., & Tosatto, S. C. E. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw315 · Cited by 415 · 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

RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles

Clementel, D., Conte, A. D., Monzón, A. M., Camagni, G. F., Minervini, G., Piovesan, D., & Tosatto, S. C. E. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac365 · Cited by 175 · 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

Exploring Biological Networks with Cytoscape Software

Yeung, N., Cline, M., Kuchinsky, A., Smoot, M. E., & Bader, G. D. (2008) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0813s23 · Cited by 78 · 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

Design and evolution of chimeric streptavidin for protein-enabled dual gold catalysis

Christoffel, F., Igareta, N. V., Pellizzoni, M. M., Tiessler‐Sala, L., Lozhkin, B. V., Spiess, D. C., Lledós, A., Maréchal, J., Peterson, R. L., & Ward, T. R. (2021) · Nature Catalysis · doi:10.1038/s41929-021-00651-9 · Cited by 73 · see citing works

Mechanical Unfolding of an Ankyrin Repeat Protein

Serquera, D., Lee, W., Settanni, G., Marszałek, P. E., Paci, E., & Itzhaki, L. S. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2009.12.4287 · Cited by 61 · 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

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 Gating Mechanism of the Serotonin 5-HT 3 Receptor

Yuan, S., Filipek, S., & Vogel, H. (2016) · Structure · doi:10.1016/j.str.2016.03.019 · Cited by 50 · see citing works

Mechanistic insights into the deleterious roles of Nasu-Hakola disease associated TREM2 variants

Dash, R., Choi, H. J., & Moon, I. S. (2020) · Scientific Reports · doi:10.1038/s41598-020-60561-x · Cited by 47 · see citing works

Structure–Function Relationships in the Human P-Glycoprotein (ABCB1): Insights from Molecular Dynamics Simulations

Lagares, L. M., Pérez‐Castillo, Y., Minovski, N., & Novič, M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms23010362 · Cited by 44 · see citing works

Mapping the human protein interactome

Figeys, D. (2008) · Cell Research · doi:10.1038/cr.2008.72 · Cited by 44 · see citing works

Bacterial Ammeline Metabolism via Guanine Deaminase

Seffernick, J. L., Dodge, A. G., Sadowsky, M. J., Bumpus, J. A., & Wackett, L. P. (2009) · Journal of Bacteriology · doi:10.1128/jb.01243-09 · Cited by 38 · see citing works

Genetic interaction mapping informs integrative structure determination of protein complexes

Braberg, H., Echeverria, I., Bohn, S., Cimermancic, P., Shiver, A., Alexander, R., Xu, J., Shales, M., Dronamraju, R., Jiang, S., et al. (2020) · Science · doi:10.1126/science.aaz4910 · Cited by 37 · see citing works

X-ray Structure and Mutational Analysis of the Atrazine Chlorohydrolase TrzN

Seffernick, J. L., Reynolds, E., Fedorov, A. A., Fedorov, E. V., Almo, S. C., Sadowsky, M. J., & Wackett, L. P. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.138677 · Cited by 36 · see citing works

Screening of the Prime bioactive compounds from Aloe vera as potential anti-proliferative agents targeting DNA

Majumder, R., Das, C. K., Banerjee, I., Jena, B. C., Mandal, A., Das, P., Pradhan, A. K., Das, S., Basak, P., Das, S. K., et al. (2021) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2021.105052 · Cited by 31 · see citing works

RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction

Brysbaert, G., Lorgouilloux, K., Vranken, W., & Lensink, M. F. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx586 · Cited by 26 · see citing works

Adaptive Steered Molecular Dynamics Combined With Protein Structure Networks Revealing the Mechanism of Y68I/G109P Mutations That Enhance the Catalytic Activity of D-psicose 3-Epimerase From Clostridium Bolteae

Zhu, J., Li, Y., Wang, J., Yu, Z., Liu, Y., Tong, Y., & Han, W. (2018) · Frontiers in Chemistry · doi:10.3389/fchem.2018.00437 · Cited by 25 · see citing works

Artificially expanded genetic information systems (AEGISs) as potent inhibitors of the RNA-dependent RNA polymerase of the SARS-CoV-2

Jena, N. R., Pant, S., & Srivastava, H. K. (2021) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2021.1883112 · 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

Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins

Laulumaa, S., Nieminen, T., Raasakka, A., Krokengen, O. C., Safaryan, A., Hallin, E. I., Brysbaert, G., Lensink, M. F., Ruskamo, S., Vattulainen, I., et al. (2018) · BMC Structural Biology · doi:10.1186/s12900-018-0087-2 · Cited by 22 · see citing works

In Silico Insights into Protein–Protein Interaction Disruptive Mutations in the PCSK9-LDLR Complex

Martin, W. R., Lightstone, F. C., & Cheng, F. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21051550 · Cited by 22 · see citing works

Dissecting the evolvability landscape of the CalB active site toward aromatic substrates

Santos, Y. L. D. L., Chew-Fajardo, Y. L., Brault, G., & Doucet, N. (2019) · Scientific Reports · doi:10.1038/s41598-019-51940-0 · Cited by 21 · see citing works

N ‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study

Mathew, A. T., Baidya, A. T. K., Das, B., Devi, B., & Kumar, R. (2022) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26417 · Cited by 21 · see citing works

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

Nepomnyachiy, S., Ben-Tal, N., & Kolodny, R. (2015) · Structure · doi:10.1016/j.str.2015.02.013 · Cited by 20 · see citing works

Identification of Key Residues in Proteins Through Centrality Analysis and Flexibility Prediction with RINspector

Brysbaert, G., Mauri, T., de Ruyck, J., & Lensink, M. F. (2018) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.66 · Cited by 18 · see citing works

Immersive Analytics Applications in Life and Health Sciences

Czauderna, T., Haga, J., Kim, J., Klapperstück, M., Klein, K., Kuhlen, T., Oeltze‐Jafra, S., Sommer, B., & Schreiber, F. (2018) · Lecture notes in computer science · doi:10.1007/978-3-030-01388-2_10 · Cited by 16 · see citing works

Inhibition of the RNA-dependent RNA Polymerase of the SARS-CoV-2 by Short Peptide Inhibitors

Pant, S., & Jena, N. R. (2021) · European Journal of Pharmaceutical Sciences · doi:10.1016/j.ejps.2021.106012 · Cited by 16 · see citing works

Codon usage is less optimized in eukaryotic gene segments encoding intrinsically disordered regions than in those encoding structural domains

Homma, K., Noguchi, T., & Fukuchi, S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw899 · Cited by 15 · see citing works

Role of a high centrality residue in protein dynamics and thermal stability

Almeida, V. M., Chaudhuri, A., Cardoso, M. V. C., Matsuyama, B. Y., Ferreira, G. M., Trossini, G. H. G., Salinas, R. K., Loria, J. P., & Marana, S. R. (2021) · Journal of Structural Biology · doi:10.1016/j.jsb.2021.107773 · Cited by 14 · see citing works

M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study

Zeba, A., Sekar, K., & Ganjiwale, A. D. (2023) · Genomics & Informatics · doi:10.5808/gi.23035 · Cited by 13 · see citing works

SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations

Bedart, C., Renault, N., Chavatte, P., Porcherie, A., Lachgar, A., Capron, M., & Farce, A. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00854 · Cited by 13 · see citing works

Insights into the role of d ‐amino acid oxidase mutations in amyotrophic lateral sclerosis

Padhi, A. K., & Hazra, S. (2018) · Journal of Cellular Biochemistry · doi:10.1002/jcb.27529 · Cited by 13 · see citing works

Mechanistic insights into the loss-of-function mechanisms of rare human D-amino acid oxidase variants implicated in amyotrophic lateral sclerosis

Padhi, A. K., & Zhang, K. Y. J. (2020) · Scientific Reports · doi:10.1038/s41598-020-74048-2 · Cited by 12 · see citing works

Conformational plasticity and evolutionary analysis of the myotilin tandem Ig domains

Puž, V., Pavšič, M., Lenar≷cic̆, B., & Djinović‐Carugo, K. (2017) · Scientific Reports · doi:10.1038/s41598-017-03323-6 · Cited by 12 · see citing works

Characterization of structural and functional role of selenocysteine in selenoprotein H and its impact on DNA binding

Barage, S. H., Deobagkar, D. D., & Baladhye, V. B. (2018) · Amino Acids · doi:10.1007/s00726-018-2543-5 · Cited by 12 · see citing works

Understanding the binding specificities of mRNA targets by the mammalian Quaking protein

Sharma, M., Sharma, S., & Alawada, A. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz877 · Cited by 12 · see citing works

Integrative visual analysis of protein sequence mutations

Doncheva, N. T., Klein, K., Morris, J. H., Wybrow, M., Domingues, F. S., & Albrecht, M. (2014) · BMC Proceedings · doi:10.1186/1753-6561-8-s2-s2 · Cited by 11 · see citing works

Computational Tools for the Interactive Exploration of Proteomic and Structural Data

Morris, J. H., Meng, E. C., & Ferrin, T. E. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r000007-mcp201 · Cited by 11 · see citing works

Enhanced metastable state models of TAM kinase binding to cabozantinib explains the dynamic nature of receptor tyrosine kinases

Naresh, G. K. R. S., & Guruprasad, L. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1730968 · Cited by 11 · see citing works

Structure‐guided engineering of protein stability through core hydrophobicity

Ravichandran, A., Puri, A., Bhate, S. H., Habibullah, B. I., Singh, G. P., & Das, R. (2025) · Protein Science · doi:10.1002/pro.70360 · Cited by 9 · see citing works

Epidemiological and ES cell‐based functional evaluation of BRCA2 variants identified in families with breast cancer

Sullivan, T. L., Thirthagiri, E., Chong, C., Stauffer, S., Reid, S. W., Southon, E. A., Hassan, T., Ravichandran, A., Wijaya, E., Lim, J., et al. (2020) · Human Mutation · doi:10.1002/humu.24154 · Cited by 8 · see citing works

Structural and functional impact of missense mutations in TPMT: An integrated computational approach

Fazel-Najafabadi, E., Ahar, E. V., Fattahpour, S., & Sedghi, M. (2015) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2015.09.004 · Cited by 8 · see citing works

Residue interaction networks of K-Ras protein with water molecules identifies the potential role of switch II and P-loop

Kumar, S. U., & Doss, C. G. P. (2021) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2021.104597 · Cited by 8 · see citing works

Molecular Insights into the Heterotropic Allosteric Mechanism in Cytochrome P450 3A4-Mediated Midazolam Metabolism

Fu, T., Zhang, H., & Zheng, Q. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c01264 · Cited by 7 · see citing works

In silico analysis of SLC3A1 and SLC7A9 mutations in Iranian patients with Cystinuria

Mahdavi, M., Koulivand, L., Khorrami, M., Mirsafaie, M., & Kheirollahi, M. (2018) · Molecular Biology Reports · doi:10.1007/s11033-018-4269-6 · Cited by 7 · see citing works

Allosteric modulation of the chemokine receptor-chemokine CXCR4-CXCL12 complex by tyrosine sulfation

Sonawani, A., Kharche, S., Dasgupta, D., & Sengupta, D. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.03.078 · Cited by 6 · see citing works

Computational characterization of the binding mode between oncoprotein Ets‐1 and DNA‐repair enzymes

de Ruyck, J., Brysbaert, G., Villeret, V., Aumercier, M., & Lensink, M. F. (2018) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25578 · Cited by 5 · see citing works

Structural Basis and Mechanism for Vindoline Dimers Interacting with α,β-Tubulin

Zhang, Z., Lu, C. J., Wang, P., Li, A., Zhang, H., & Xu, S. (2019) · ACS Omega · doi:10.1021/acsomega.9b00947 · Cited by 6 · see citing works

cddApp: a Cytoscape app for accessing the NCBI conserved domain database

Morris, J. H., Wu, A., Yamashita, R. A., Marchler‐Bauer, A., & Ferrin, T. E. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu605 · Cited by 5 · see citing works

A new compound heterozygous mutation in GJB2 causes nonsyndromic hearing loss in a consanguineous Iranian family

Keivani, A., Haghighat-Nia, A., Fazel-Najafabadi, E., Hosseinzadeh, M., & Salehi, M. (2015) · International Journal of Pediatric Otorhinolaryngology · doi:10.1016/j.ijporl.2015.01.027 · Cited by 5 · see citing works

Destabilization of EpCAM dimer is associated with increased susceptibility towards cleavage by TACE

Žagar, T., Pavšič, M., & Gaber, A. (2021) · PeerJ · doi:10.7717/peerj.11484 · Cited by 5 · see citing works

Analysis of Protein Structures Using Residue Interaction Networks

Shcherbinin, D., & Veselovsky, A. V. (2019) · Challenges and advances in computational chemistry and physics · doi:10.1007/978-3-030-05282-9_3 · Cited by 5 · see citing works

Computational vaccinology approach: Designing an efficient multi-epitope peptide vaccine against Cryptococcus neoformans var. grubii’s heat shock 70KDa proteinPreprint

Elhassan, R. M., Alsony, N. M., Othman, K. M., Izz-Aldin, D. T., Alhaj, T. A., Ali, A. A., Abashir, L. A., Ahmed, O. H., & Hassan, M. A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/534008 · Cited by 5 · see citing works

Design, construction and in vivo functional assessment of a hinge truncated sFLT01

Zakeri, F., Latifi‐Navid, H., Soheili, Z., Sadeghi, M., Arab, S. S., Samiei, S., Pirmardan, E. R., Taghizadeh, S., Ahmadieh, H., & Hafezi‐Moghadam, A. (2022) · Gene Therapy · doi:10.1038/s41434-022-00362-1 · Cited by 4 · see citing works

Towards Computationally Guided Design and Engineering of a Neisseria meningitidis Serogroup W Capsule Polymerase with Altered Substrate Specificity

Paudel, S., Wachira, J., & McCarthy, P. C. (2021) · Processes · doi:10.3390/pr9122192 · 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

Network modeling in systems biology

Xia, T. (2010) · doi:10.31274/etd-180810-4318 · Cited by 3 · see citing works

Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer

Pavšič, M. (2021) · Data in Brief · doi:10.1016/j.dib.2021.107403 · Cited by 3 · see citing works

GEMIN4 Variants: Risk Profiling, Bioinformatics, and Dynamic Simulations Uncover Susceptibility to Bladder Carcinoma

Mohamed, A., Salama, A. F., Sabaa, M. A., Toraih, E. A., & Elshazli, R. M. (2024) · Archives of Medical Research · doi:10.1016/j.arcmed.2024.102970 · Cited by 2 · see citing works

Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26Preprint

Salerno-Kochan, A., Horn, A., Ghosh, P., Nithin, C., Kościelniak, A., Strauß, D., Roßbach, O., Bujnicki, J. M., Gaik, M., Medenbach, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.20.461029 · Cited by 2 · see citing works

Proposed mechanism for Rft1-mediated scrambling of a dolichol-linked oligosaccharide

Chiduza, G. N., Sakata, K.-T., Wolfe, H. G., Noor, F., & Menon, A. (2025) · bioRxiv · doi:10.1002/pro.70715 · Cited by 3 · see citing works

Tau protein misfolding and aggregation induced by abnormal N-glycosylation: Insights from Molecular dynamics simulation studies.Preprint

Alen Mathew, T., Anurag Baidya, T. K., Das, B., Devi, B., & Kumar, R. (2022) · doi:10.22541/au.165694694.45718052/v1 · Cited by 1 · see citing works

Mechanism-guided mutagenesis of Rft1 to test its role as a dolichol-linked oligosaccharide scramblase in cellsPreprint

Chiduza, G. N., Sakata, K., Wolfe, H. G., Noor, F., & Menon, A. K. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.07.692794 · Cited by 1 · see citing works

Hydrocarbon biosynthesis by bacteria : genes and hydrocarbon products.

Sukovich, D. J. (2010) · University of Minnesota Digital Conservancy (University of Minnesota)

KINETIC CHARACTERIZATION AND NEWLY DISCOVERED INHIBITORS FOR VARIOUS CONSTRUCTS OF HUMAN T-CELL LEUKEMIA VIRUS-I PROTEASE AND INHIBITION EFFECT OF DISCOVERED MOLECULES ON HTLV-1 INFECTED CELLS

Yorulmaz, A. (2010) · VTechWorks (Virginia Tech)

Computational Methods for Signal Transduction

Scardoni, G., Tosadori, G., Morris, J., Pratap, S., Laudanna, C., & Han, A. A. (2019) · doi:10.1002/9781119060208.ch7

Structural characterization and selective drug targeting of higher-order DNA G-quadruplex systems.

Monsen, R. C. (2020) · doi:10.18297/etd/3553

Peer Review #1 of "Destabilization of EpCAM dimer is associated with increased susceptibility towards cleavage by TACE (v0.1)"

(2021) · PeerJ · doi:10.7287/peerj.11484v0.1/reviews/1

Peer Review #2 of "Destabilization of EpCAM dimer is associated with increased susceptibility towards cleavage by TACE (v0.1)"

(2021) · PeerJ · doi:10.7287/peerj.11484v0.1/reviews/2

Relaciones de estructura-función en la P-glicoproteína humana (ABCB1): Perspectivas de las simulaciones de dinámica molecular

Lagares, L. M., Pérez‐Castillo, Y., Minovski, N., & Novič, M. (2022) · Magna Scientia UCEVA · doi:10.54502/msuceva.v2n2a5

Investigation of the Behaviors of Some Newly Designed Ligands in the Epstein Barr EBNA1/DNA Binding Domain by MD Simulations and Binding Free Energy Calculations

Ercan, S. (2025) · Advanced Theory and Simulations · doi:10.1002/adts.202500371

Chimera X Interface to Enhance Understanding in Biochemistry and Immunology

DALPIAZ, G., Schiling, K. M., Eduarda, G., da Silva, A. A., & Meireles, M. R. (2025) · Biochemistry and Molecular Biology Education · doi:10.1002/bmb.70025

A novel trinuclear copper(II) complex bearing mono- and dianionic 5-fluorouracil ligands: Synthesis, crystal structure, Hirshfeld surface analysis, and in silico assessment of thymidylate synthase inhibition

Icsel, C., Ercan, S., Aygun, M., & Yilmaz, V. T. (2025) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2025.144803

Site-specific evaluation of mutation-based mimics of histone glycation in the nucleosome

Dalilah, Y., & Simm, A. (2026) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2026.1838713

Applications Note structureViz: Linking Cytoscape and UCSF Chimera

Morris, J. H., Huang, C. C., Babbitt, P. C., Ferrin, T. E., & Lengauer, T. (2016)

Bioinformatics Advance Access published July 10, 2007 structureViz: Linking Cytoscape and UCSF Chimera

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

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

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