Publications

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Professional research reports:

•Co-author. WHO Guidelines for the prequalification assessment of insecticide-treated nets 

•Co-author. Patient-centric approaches in public health: the opportunity for large scale deployment of mHealth solutions. Frontiers in Public Health 2022, submitted.

•Co-author. Country support process and lessons learnt. D4.6 and D4.4 deliverables of European mHealth and Innovation Hub, European Commission Coordinated and Support Action under Horizon 2020. Available at: https://mhealth-hub.org/documents

•Contribution to “WHO’s role in SARS-CoV-2 laboratory diagnostics: an end-to-end approach” , Weekly Epidemiological Record, No 16, 23 April 2021, pages 125-137 , as part of WHO COVID Laboratory Diagnostics Team (ACT Dx R&D WG). Available at: https://apps.who.int/iris/bitstream/handle/10665/340940/WER9616-125-132-eng-fre.pdf?sequence=1&isAllowed=y

•Contribution to “Digital health platform handbook: building a digital information infrastructure (‎infostructure)‎ for health”, World Health Organization 2021, as part of Be He@lthy Be Mobile Team. Available at: https://apps.who.int/iris/handle/10665/337449

• Contribution to the “Digital tools for COVID-19 contact tracing. Annex: Contact tracing in the context of COVID-19 (2 June 2020)”, World Health Organization , available at: https://apps.who.int/iris/bitstream/handle/10665/332265/WHO-2019-nCoV-Contact_Tracing-Tools_Annex-2020.1-eng.pdf?sequence=1&isAllowed=y

•Penholder EC H2020 topics

(Author):Demonstrating the potential & benefits of a European Digital Health, Infrastructure for Personalised Medicine (PM),AI for Health Imaging,Coordination & Support to better data& secure cross-border digital infrastructures building on European capacities for genomics &PM,Accelerating the uptake of in-silico clinical trials for testing medicines.

(Co-Author):The Smart Hospital Of The Future

•Drafting EC Horizon Europe Missions & Health Cluster programme

(Author & Co-Author):DigDigital Twins, Improvement of Personalized Treatment and Prevention of Disease through Digital Innovation,Digital technologies for Personalized Cancer Prediction, Augmented self,Antimicrobial resistance,Polypharmacy

•EC Topic coordinator:Exploiting the full potential of in-silico medicine research for personalised diagnostics & therapies in cloud-based environments (cross-sectional & multidisciplinary data)

•EC communication:Digital transformation of health &care.Assistant

Co-Author for Roadmap & Action Plan European Health Data Infrastructure.TaskForce DigiCare

•EC PM staff working document (SWD).Co-author

•AI and health.EC CNECT/H3 note.Co-author

•EC text for conference on Data Donation for Health.Co-author

•EC EOSC SWD.Co-author.Preparation meeting Health Research Innovation Cloud with stakeholders in collaboration with DG RTD

•Genomics EC static page& infographic.Co-author

•Healthy measures conference on PM.Invited speaker.Report assistance

•Report assistance:impact of IoT & wearables on integrated care & ageing (collaboration with OECD).Prospective development of the new healthcare ecosystem composed by IoT,cloud based services,mobile apps,wearables (sensors & actuators),HPC,DSS & new AI systems

•Briefings for Comissioner M.Gabriel,PGEU,EAPM,BiodataWorldCongress,Elixir,Genomics event UK/Estonia…

Communicating science to policy makers.Feeding policy with research results.

Keynote speeches & chairing session/roundtable (Author):

-Personalised Medicine 2018,Healthy Measures.Can value-based healthcare be implemented in Europe? How PM & patient outcomes can help.Panel discussions:Healthcare Financing based on Value &Outcomes-based Healthcare Systems.Patient data as fuel for PM to discuss the benefits-to patients,entrepreneurs,governments & society-of use of patient data for prescribing the right drugs for a patient,at the right doses,tailored for their specific genetic make-up for better outcomes while reducing costs.Stakeholders,policy makers,industry

-National Congress of Portuguese Pharmacies 2018.Debate Healthcare financing,Innovation,Healthy living& Digital Health in the pharmacy community.E-health solutions in European Community Pharmacies.Pharmacies,pharmacists,other health care professionals & health stakeholders,decision makers and members of the national parliament & Government.The Portuguese National Association of Pharmacies represents 95% of the Portuguese community pharmacies,one of the most developed in Europe in matters concerning pharmaceutical policies

-ISPOR 2018.Health care X.0:digital technologies & creation of value.Panel.Potential of digital technologies in creating & delivering better value in healthcare.Opportunities for health economics & outcomes researchers to participate in co-creation of the “next healthcare system”.Discussion:Healthcare innovation,value &evidence-based medicine,managing &measuring impact of digital health technologies

-VPH Conference 2018.Awareness of regulation of in silico methods & medical devices for in silico clinical trials, as a complement of in vivo & in vitro tools to reduce/partially replace animal testing.FDA,VPH Institute,Avicenna Alliance stakeholders.I Presented EC future priorities of in silico medicine & digital transformation of health & care

-Series of Meetings with MS Representatives of the Signatories of the Declaration:‘Towards access to at least 1 million sequenced genomes in the European Union by 2022’.Co-author.Landscape for genomic data/infrastructures in Europe

Medical writer associated to Editor

Journal of the CPhi worldwide conference, 4-6 October 2016, BCN

http://viewer.zmags.com/publication/3f349b29#/3f349b29/4

http://viewer.zmags.com/publication/6bfe9969#/6bfe9969/4

http://viewer.zmags.com/publication/6bfe9969#/6bfe9969/6

Early achievements track-record

https://www.researchgate.net/profile/Violeta_Perez-Nueno

http://scholar.google.es/citations?user=NIewN_UAAAAJ&hl=en

http://www.researcherid.com/rid/F-3968-2016

http://orcid.org/0000-0003-3558-5267

Patent Publications

  • European patent EP14305 487.2 – 1464. May 28, 2015. New derivatives of cephalosporin for treatment of cancer. A.S. Karaboga, V.I. Pérez-Nueno, M. Souchet.
  • ES Patent ES200602764. Oct. 26, 2006 (PCT ES2007/000613. Oct. 26, 2007). WO 2008/049950 May 2, 2008 (EP, US, Canada and Japan extension). Novel polynitrogenated systems as anti-HIV agents. J. Teixidó, J.I. Borrell, S. Nonell, X. Batllori, S. Pettersson, L. Ros, R. Puig de la Bellacasa, M.O. Rabal, V.I. Pérez-Nueno, J. Esté, I. Clotet, M. Armand-Ugón.

Peer-Reviewed Publications (Total=28, h-index=16, i10-index=22, total citations=672). Impact factor; number of citations in parentheses (IF;NC). Published in the top journals in my domain.

First Author (Total=16, 58%) (* Implies also corresponding author)

(3.1;1)* Towards the Integration of Quantitative and Systems Pharmac.. Curr Pham Des. 2016 (22) 6881-84.

(3.9;17)* GESSE: Predicting Drug Side Effects From Drug-Target… J. Chem. Inf. Model. 2015 (55) 1804-23.

(4.7;18)* Using quantitative systems pharmacology for novel dr… Expert Opin. Drug Discov. 2015 (10) 1-17.

(3.9;15)* GES polypharmacology fingerprints: A novel approach f… J. Chem. Inf. Model. 2014 (54) 720-34.

(3.9;19)* Detecting Drug Promiscuity using Gaussian Ensemble … J. Chem. Inf. Model. 2012 (52) 1948-61.

(4.7;16)* Identifying and characterizing promiscuous targets: I… Expert Opin. Drug Discov. 2012 (7) 1-17.

(NA;6)* Predicting Drug Promiscuity Using … The Open Conference Proceedings Journal 2011 (2) 113-29.

(3.9;39)* Using Consensus-Shape Clustering to Identify Promisc… J. Chem. Inf. Model. 2011 (51) 1233-48.

(4.6;8)* Predicting drug polypharmacology using a no… Journal of Cheminformatics 2011(3, Suppl 1): O19.

(2.4;10)* Using spherical harmonic surface property representati… Molecular Informatics 2011 (30) 151–59.

(2.6;4)* Applying in silico Tools to the Discovery of Novel CXCR4 In… Drug Dev. Res. 2011 (72) 95–111.

(3.9;100) A Comprehensive Comparison of Ligand-Based Virtual … J. Chem. Inf. Model. 2010 (50) 2079-93.

(3.9;63) APIF: A New Interaction Fingerprint Based on Atom Pai… J. Chem. Inf. Model. 2009 (49) 1245-60.

(3.9;40) Discovery of Novel HIV Entry Inhibitors for the CXCR4 … J. Chem. Inf. Model. 2009 (49) 810-23. In LeadDiscovery’s DailyUpdates (Infectious Diseases) June 2009.

(3.9;36) Clustering and classifying diverse HIV entry inhibitors u… J. Chem. Inf. Model. 2008 (48) 2146-65.

(3.9;77) Comparison of Ligand-Based and Receptor-Based Virtual… J. Chem. Inf. Model. 2008 (48) 509-33.

Corresponding Author (Total=15, 58%)

(2;12) Studying the Binding Interactions of Allosteric Agonists and … J. Mol. Graph. Model. 2015 (60) 1-14.

(NA;0) Polypharmacology within CXCR4: Multiple binding sites a… AIP Conf. Proc. 2014 (1618) 1036-38.

(3.9;16) Highly specific and sensitive pharmacophore model for id… J. Chem. Inf. Model. 2013 (53) 1043-56.

(2.3;22) Impact of the CXCR4 structure on docking-based virtual s… J. Mol. Graph. Model. 2012 (38) 123-36.

(3.9;19) Improving VEGFR-2 docking-based screening by pharma… J. Chem. Inf. Model. 2011 (51) 777–87.

Second Author (Total=5, 19%)

(3.7;13) Recent trends and future prospects in computational G… Curr. Top. Med. Chem. 2013 (13) 1069-97.

(2.6;26) Recent Trends and App… Combinatorial Chemistry & High Throughput Screening 2012 (15) 749-69.

(3.3;21) Novel Monocyclam Derivatives as HIV Entry Inhibitors: Desi… ChemMedChem 2010 (5) 1272-81.

(3.3;21) Biological profiling of anti-HIV agents and insights into CCR… ChemMedChem 2009 (4) 1153-63.

(3.3;19) Discovery of novel non-cyclam polynitrogenated CXCR4 cor… ChemMedChem 2008 (3) 1549–57. In Spotlights (Antiviral Agents), Angew. Chem. Int. Ed. 2008 (47) 8554-55.

Middle Author (Total=1, 4%)

(3.9;18) Computational proteomics pitfalls and challenges: Hava… Journal of Proteomics 2013 (87) 134-38.

Book chapters

(3;1) Spherical Harmonic Molecular Surfaces (ParaFit). Ritchie, D.W.; Pérez-Nueno, V.I. (2012) in Scaffold Hopping in Medicinal Chemistry, chapter 3d (editor Nathan Brown). Methods and Principles in Medicinal Chemistry series, “Bioisosteres in Medicinal Chemistry”. Wiley-VCH Publishing,London, UK, pp.183-193.

Executive Guest Editor Current Pharmaceutical Design (Impact Factor 3.452)

Thematic Issue “Towards the integration of Quantitative and Systems Pharmacology into drug discovery: a systems level understanding of therapeutic and toxic effects of drugs”

Editorial Writing. http://www.eurekaselect.com/149485/article

Journal Covers

http://violetaisabel-perez-nueno.com/art-covers/ ‎

  • Journal of Chemical Information and Modeling (2015), volume 55, issue 9.
  • Contribution to Journal of Chemical Information and Modeling (2015), volume 55, issue 1.
  • Journal of Chemical Information and Modeling (2014), volume 54, issue 3.
  • Journal of Chemical Information and Modeling (2008), volume 48, issue 3.

Selected Conference Presentations (Total=48 , see Links & Others )

Oral Communication (Total=14)

2016 April, 4th Int. Work-Conf. on Bioinformatics and Biomedical Engineering (IWBBIO), Granada, Spain

2015 April, 3rd Int. Work-Conf. on Bioinformatics and Biomedical Engineering (IWBBIO), Granada, Spain

2014 April, 10th Int. Conf. Comput. Meth. in Sciences and Engineering (ICCMSE), Athens, Greece (3 talks)

2013 October, Journées de la
Société Francophone de Chémoinformatique, Nancy, France

2012 May, 15th Hellenic Symposium on Medicinal Chemistry, Athens, Greece

2012 March, 243rd ACS National Meeting, San Diego, California, USA

2012 March, Medicinal Chemistry Conference, Lanzarote, Spain

2011 October, 5emes Journées Nationales de Chémoinformatique, Cabourg, France

2011 June, 9th International Conference on Chemical Structures, Noordwijkerhout, Netherlands

2010 November, 6th German Conference on Chemoinformatics, Goslar, Germany

2010 July, 5th Joint Sheffield Conference on Chemoinformatics, Sheffield, England

2008 September, XXth International Symposium on Medicinal Chemistry (EFMC-ISMC), Vienna, Austria

Invited Speaker (Total=17)

2015 September, Seminar Molécules Thérapeutiques in silico (MTi), Université Paris Diderot, Paris, France

2013 September, 246th ACS National Meeting, Indianapolis, Indiana, USA (2 talks)

2012 December, Bioinformatics and OMICS, La Havana, Cuba (2 talks)

2012 October, Journees Ouvertes MBI.Modélisation des Biomolécules et de leurs Interactions, Nancy,France

2012 March, Lecture inside Master “Introduction to the process of drug discovery”, Research and technological centre for chemistry and pharmaceutical industry (IUCT), Barcelona, Spain

2012 March, Seminar,Institute for Research in Biomedicine-Barcelona Science Park (IRB), Barcelona, Spain

2011 November, Séminaires & Conférences Chimie École Doctorale, Université Montpellier II, France

2011 October, Lecture inside Master in Chemoinformatics “In silico drug design”, Strasbourg, France

2011 March, Lecture inside Master “Introduction to the process of drug discovery”, IUCT, Barcelona, Spain

2011 February, 3rd International Conference on Drug Discovery & Therapy, Dubai, UAE

2010 November, Chemoinformatics seminar, Inst. Munic. d’Investigació Mèdica (IMIM), Barcelona, Spain

2010 March, Lecture inside Master “Introduction to the process of drug discovery”, IUCT, Barcelona, Spain

2010 March, Cepos Symposium, Portsmouth, England

2009 September, Model(l)ing´09, Annual Molecular Modelling Workshop & Annual International Meeting of the MGMS, Erlangen, Germany

2009 January, Seminar BINGO, Lorraine Research Lab Comput. Scie. and its App. (LORIA), Nancy, France

Poster (Total=17)

2015 April, 3rd Int. Work-Conf. on Bioinformatics and Biomedical Engineering (IWBBIO), Granada, Spain

2014 April,10th Int. Conf. Comput. Meth. in Sciences and Engineering (ICCMSE),Athens,Greece (2 posters)

2013 October, Journées de la
Société Francophone de Chémoinformatique, Nancy, France

2013 September, 246th ACS National Meeting, Indianapolis, Indiana, USA

2013 July, 49th Drug Discovery and Selection 
RICT, Nice, France

2012 March, 243rd ACS National Meeting, San Diego, California, USA

2012 March, Medicinal Chemistry Conference, Lanzarote, Spain

2011 February, 3rd International Conference on Drug Discovery & Therapy, Dubai, UAE

2010 September, 18th EuroQSAR, Rhodes, Greece

2010 September, XXIst International Symposium on Medicinal Chemistry, Brussels, Belgium

2010 July, 3DSIG 2010. Structural Bioinformatics and Computational Biophysics, Boston, USA

2010 July, 5th Joint Sheffield Conference on Chemoinformatics, Sheffield, England

2008 April, Targeting and Tinkering with Interaction Networks, Barcelona Biomed Conferences, Spain

2007 July, AIMECS07, 6th AFMC International Medicinal Chemistry Symposium, Istambul, Turkey

2007 July, 4th Joint Sheffield Conference on Chemoinformatics, Sheffield, England

2007 October, Virtual Discovery Europe. Computer-Aided Drug Design & Screening, London, England

List with Five Main Publications

My author position is in bold font and corresponding authors underlined.

(IF: Impact Factor, NC: Number of Citations).

Click on the highlighted text if you wish to follow the link.

  • Pettersson, S.; Pérez-Nueno, V. I.; Ros-Blanco, L.; Puig de la Bellacasa, R.; Rabal,O.; Batllori, X.; Clotet, B.; Clotet-Codina, I.; Armand-Ugón, M.; Esté, J.; Borrell, J. I.; Teixidó, J. Discovery of novel non-cyclam polynitrogenated CXCR4 coreceptor inhibitors. In Spotlights (Antiviral Agents), Chem. Int. Ed. 2008, 47, 8554-8555. (IF: 12.7) [PDF] and ChemMedChem 2008, 3, 1549-1557. (IF: 3.3, NC:15) [PDF]

Angewandte Chemie is the top journal in the category “Chemistry, Multidisciplinary” that publishes original research according to Journal Citation Reports (JCR). ChemMedChem is 8th out of 40 medicinal chemistry journals listed by ISI in this category. This work was done in collaboration with experimental colleagues and reports a prospective application of computational methods that I previously developed. It led to the patent WO 2008/049950.

  • Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W. Predicting drug polypharmacology using a novel surface property similarity-based approach. Journal of Cheminformatics 2011(3, Suppl 1): O19 (IF: 4.6, NC:8) [PDF]

Journal of Cheminformatics is standing in my field. 4th out of 194 journals in the computer science applications category in 2012 Journal Citation Reports (JCR). The work fully developed from this original idea has been published in two JCIM papers (1rst ranked in the category), appearing also as Front Cover Illustration for the JCIM 2014 (54) Issue 3 and 2015 (55) Issue 9. The application of the methods shown in the paper for anti-cancer compounds led to the patent EP14305 487.2

  • Pérez-Nueno, V.I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W. A Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Dataset Reveals Limitations of Current 3D Methods. Chem. Inf. Model. 2010, 50, 2079-93. (IF: 3.9, NC:69) [PDF]

Chem. Inf. Model. is top journal in my field. It ranked 1st out of 99 journals in the Computer Science Interdisciplinary Applications category of the 2011 Journal Citation Reports (JCR). Notice the high number of citations so far for this controversial paper.

  • Pérez-Nueno, V. I.; Ritchie, D. W.; Rabal, O.; Pascual, R.; Borrell, J. I.; Teixidó, J. Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape matching and Ligand-Receptor Docking. Chem. Inf. Model. 2008, 48, 509-533, & Cover Illustration. (IF: 3.9, NC:55) [PDF]

Chem. Inf. Model. is top journal in my field. It ranked 1st out of 99 journals in the Computer Science Interdisciplinary Applications category of the 2011 Journal Citation Reports (JCR). Notice the high number of citations so far for this paper. It also appeared as Front Cover Illustration for the JCIM 2008 (48) Issue 3.

  • Pérez-Nueno, V. I.; Rabal, O.; Borrell, J. I.; Teixidó, J. APIF: A New Interaction Fingerprint Based on Atom Pairs and its Application to Virtual Screening. Chem. Inf. Model. 2009, 49, 1245-1260. (IF: 3.9, NC:41) [PDF]

Chem. Inf. Model. is top journal in my field. It ranked 1st out of 99 journals in the Computer Science Interdisciplinary Applications category of the 2011 Journal Citation Reports (JCR)). Notice the high number of citations so far for this paper, mostly in studies presenting new models following the proposed approach.

Full References of the List of Peer-Reviewed Publications (Total 26)

Publications from Thesis

Legend: Original Articles (OA), Review Articles (RA) and peer-reviewed Proceedings Papers (PP).

My author position is in bold font and corresponding authors underlined.

(IF: Impact Factor, NC: Number of Citations)

  1. Pettersson, S.; Pérez-Nueno, V. I.; Ros-Blanco, L.; Puig de la Bellacasa, R.; Rabal,O.; Batllori, X.; Clotet, B.; Clotet-Codina, I.; Armand-Ugón, M.; Esté, J.; Borrell, J. I.; Teixidó, J. Discovery of novel non-cyclam polynitrogenated CXCR4 coreceptor inhibitors. In Spotlights (Antiviral Agents), Angew. Chem. Int. Ed. 2008 (47) 8554-55. (IF: 12.7) and ChemMedChem 2008 (3) 1549–57. (IF: 3.3, NC:15) (OA)
  2. Pérez-Nueno, V. I.; Ritchie, D. W.; Rabal, O.; Pascual, R.; Borrell, J. I.; Teixidó, J. Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape matching and Ligand-Receptor Docking. J. Chem. Inf. Model. 2008 (48) 509-33, and Front Cover Illustration. (IF: 3.9, NC:55) (OA)
  3. Pérez-Nueno, V. I.; Ritchie, D. W.; Borrell, J. I.; Teixidó, J. Clustering and classifying diverse HIV entry inhibitors using a novel consensus shape based virtual screening approach: Further evidence for multiple binding sites within the CCR5 extracellular pocket. J. Chem. Inf. Model. 2008 (48) 2146-65. (IF: 3.9, NC:30) (OA)
  4. Pérez-Nueno, V. I.; Pettersson, S.; Ritchie, D. W.; Borrell, J. I.; Teixidó, J. Discovery of Novel HIV Entry Inhibitors for the CXCR4 Receptor by Prospective Virtual Screening. J. Chem. Inf. Model. 2009 (49) 810-23. (IF: 3.9, NC:31) (OA)
  5. Carrieri, A.; Pérez-Nueno, V. I.; Fano, A.; Pistone, C.; Ritchie, D. W.; Teixidó, J. Biological profiling of anti-HIV agents and insights into CCR5 antagonist binding using in silico techniques. ChemMedChem 2009 (4) 1153-63. (IF: 3.3, NC:19) (OA)
  6. Pérez-Nueno, V. I.; Rabal, O.; Borrell, J. I.; Teixidó, J. APIF: A New Interaction Fingerprint Based on Atom Pairs and its Application to Virtual Screening. J. Chem. Inf. Model. 2009 (49) 1245-1260. (IF: 3.9, NC:40) (OA)
  7. Pettersson, S.; Pérez-Nueno, V. I.; Mena, M. P.; Clotet, B.; Esté, J.; Borrell, J. I.; Teixidó, J. Novel Monocyclam Derivatives as HIV Entry Inhibitors: Design, Synthesis, Anti-HIV Evaluation, and Their Interaction with the CXCR4 Coreceptor. ChemMedChem 2010 (5) 1272-81. (IF: 3.3, NC:15) (OA)

Publications from the post doctorate(s)

  1. Pérez-Nueno, V. I. Using quantitative systems pharmacology for novel drug discovery. Expert Opin. Drug Discov. 2015 (10) 1-17. (IF: 3.6, NC:0) (RA)
  2. Pérez-Nueno, V. I. ;Souchet, M.; Karaboga,A.S.; Ritchie, D.W. GESSE: Predicting Drug Side Effects From Drug-Target Relationships. J. Chem. Inf. Model. 2015 (55) 1804-23, and Front Cover Illustration. (IF: 3.9, NC:1) (OA)
  3. Planesas, J.M.;Pérez-Nueno, V. I.;Borrell, J. I.; Teixidó, J. Studying the Binding Interactions of Allosteric Agonists and Antagonists of the CXCR4 Receptor. J. Mol. Graph. Model. 2015 (60) 1-14. (IF: 2.0, NC:0) (OA)
  4. Planesas, J.M.;Pérez-Nueno, V. I.;Borrell, J. I.; Teixidó, J. Polypharmacology within CXCR4: Multiple binding sites and allosteric behavior. AIP Conf. Proc. 2014 (1618) 1036-38. (IF: None, NC:0) (PP)
  5. Pérez-Nueno, V. I.; Karaboga,A.S.;Souchet, M.; Ritchie, D.W. GES polypharmacology fingerprints: A novel approach for drug repositioning. J. Chem. Inf. Model. 2014 (54) 720-34, and Front Cover Illustration. (IF: 3.9, NC:6) (OA)
  6. Carrieri, A.; Pérez-Nueno, V. I.; Lentini, G.; Ritchie, D.W. Recent trends and future prospects in computational GPCR drug discovery: from virtual screening to polypharmacology. Curr. Top. Med. Chem. 2013 (13) 1069-97. (IF: 3.4, NC:13) (RA)
  7. Karaboga,A.S.; Planesas, J.M.; Petronin, F.; Teixidó, J.; Souchet, M.; Pérez-Nueno, V. I. Highly specific and sensitive pharmacophore model for identifying CXCR4 antagonists. Comparison with docking and shape-matching virtual screening performance. J. Chem. Inf. Model. 2013 (53) 1043-56. (IF: 3.9, NC:4) (OA)
  8. 15. Yasset Perez-Riverola, Henning Hermjako, Oliver Kohlbacher, Lennart Martens, David Creasy, Jürgen Cox, Felipe Leprevost, Baozhen Paul Shan, Pérez-Nueno, V. I., Michal Blazejczyk, Marco Punta, Klemens Vierlinger, Pedro Valiente, Kalet Leon, Glay Chinea, Osmany Guirola, Ricardo Bringas, Gleysin Cabrera, Gerardo Guillen, Gabriel Padron, Luis Javier Gonzalez, Vladimir Besada. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report. Journal of Proteomics 2013 (87) 134-38. . (IF: 3.9, NC:16) (PP)
  9. 16. Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W. Detecting Drug Promiscuity using Gaussian Ensemble Screening. J. Chem. Inf. Model. 2012 (52) 1948-61. (IF: 3.9, NC:12) (OA)
  10. Ghemtio, L.; Pérez-Nueno, V. I.; Leroux, V.; Asses, Y.; Souchet, M.; Mavridis, L.; Ritchie, D.W. Recent Trends and Applications in 3D Virtual Screening. Combinatorial Chemistry & High Throughput Screening 2012 (15) 749-69. (IF: 1.2, NC:6) (RA)
  11. Planesas, J. M.; Pérez-Nueno, V. I.;Borrell, J. I.; Teixidó, J. Impact of the CXCR4 structure on docking-based virtual screening of HIV entry inhibitors. J. Mol. Graph. Model. 2012 (38) 123-36. (IF: 2.0, NC:15) (OA)
  12. Pérez-Nueno, V. I.; Ritchie, D.W. Identifying and characterizing promiscuous targets: Implications for virtual screening. Expert Opin. Drug Discov. 2012 (7) 1-17. (IF: 3.6, NC:13) (RA)
  13. Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W. Predicting drug promiscuity using spherical harmonic (SH) shape-based similarity comparisons. The Open Conference Proceedings Journal 2011 (2) 113-29. (IF: None, NC:6) (OA)
  14. Pérez-Nueno, V. I.; Ritchie, D.W. Using Consensus-Shape Clustering to Identify Promiscuous Ligands and Protein targets and to Choose the Right Query for Shape-Based Virtual Screening. J. Chem. Inf. Model. 2011 (51) 1233-48. (IF: 3.9, NC:31) (OA)
  15. Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W. Predicting drug polypharmacology using a novel surface property similarity-based approach. Journal of Cheminformatics 2011(3, Suppl 1): O19. (IF: 4.6, NC:8) (PP)
  16. Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Clark, T.; Ritchie, D.W. Using spherical harmonic surface property representations for ligand-based virtual screening. Molecular Informatics 2011 (30) 151–59. (IF: 2.4, NC:10) (OA)
  17. Planesas, J. M.; Claramunt, R. M.; Borrell, J. I.; Pérez-Nueno, V. I. Improving VEGFR-2 docking-based screening by pharmacophore post-filtering and similarity search post-processing. J. Chem. Inf. Model. 2011 (51) 777–87. (IF: 3.9, NC:13) (OA)
  18. Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W. A Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Dataset Reveals Limitations of Current 3D Methods. J. Chem. Inf. Model. 2010 (50) 2079-93. (IF: 3.9, NC:69) (OA)
  19. Pérez-Nueno, V. I.; Ritchie, D. W. Applying in silico Tools to the Discovery of Novel CXCR4 Inhibitors. Drug Dev. Res. 2011 (72) 95–111. (IF: 0.8, NC:4) (RA)