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2nd Zing Protein & RNA Structure Prediction Conference 2013

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The purpose of the Zing Conference on Protein and RNA Structure Prediction is to bring together eminent scholars with expertise in various fields of computational modeling and prediction of structure, as well as experimentalists interested in these subjects. The scope of the proposed Zing Conference will be much broader than Critical Assessment of Techniques for Protein Structure Prediction (CASP) meetings, which focus mostly on the analysis of the results of the CASP competition. Since computational prediction methods continuously improve and evolve towards prediction of structure of more and more complicated biological objects our conference will cover also related topics, such prediction of structure of protein complexes, protein docking; prediction of intrinsically disordered regions in proteins, RNA structure prediction and modeling of RNA-protein assemblages. New methodologies for protein structure and function prediction will be discussed, such as physics-based approaches to the structure prediction, structural flexibility models, and development of new improved coarse-grained potentials.

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Conference Sponsors


The Conference Chairs

Andrzej Kloczkowski
Ohio State University
Robert Jernigan
Iowa State University
Eshel Faraggi
Indiana University School of Medicine

Abstract Submission Deadlines

Poster Deadline – 1st October 2013

Abstract Information Abstract Template Word Format Abstract Template .pdf Format

The Venue

Occidental Grand Xcaret
Playa del Carmen, Mexico.




Transfers & Tours

1st December 2013 – 5th December 2013

Located adjacent to the spectacular eco-archeological Xcaret Park in the heart of the Riviera Maya, the Occidental Grand Xcaret offers delegates the chance to exchange ideas and develop collaborations with colleagues in the tranquil setting of the Caribbean Sea.

Xcaret Park is Mexico’s most famous eco-archeological attraction. It is a beautiful place full of culture and nature where visitors can enjoy amazing aquatic activities, cultural attractions and shows. Xcaret Park is filled with the natural beauty of the Caribbean Sea and the magic of a thousand year- old civilization. It is the perfect place to experience the best of Mexico.

Hotel Features
11 Restaurants
5 swimming pools
10 Jacuzzis
Fully Equipped Gym
Beach Club
Organized sports and activities (pádel, tennis, mini golf and archery)

Venue Rating****
Nearest AirportCancún International Airport
Transfers & Tours View Details


Plenary Speakers


Adriaan Bax
National Institutes of Health

Squeezing more protein structure out of NMR chemical shifts


Joel Sussman
The Weizmann Institute of Science

Structure Based Drug Design – Can X-ray Data Lead to Erroneous Predictions?


John L Markley
University of Wisconsin-Madison

Protein metamorphism: experiments and predictions


John Moult
University of Maryland

10 CASP Experiments: Successes, Bottlenecks, and Challenges in Protein Structure Modelling


Alfonso Valencia
Spanish National Cancer Research Centre

Prediction and Analysis of Protein Interaction Networks


Chris  Sander
Memorial Sloan-Kettering Cancer Center


Keith Dunker
Indiana University

Advantages of Intrinsic Disorder for Protein Function

Invited Speakers

SpeakerAffiliationPresentation Title
Adam LiwoUniversity of GdanskEssential Role of Mean-Field Electrostatic Interactions in Free Modeling of Protein and Nucleic Acid Structures at Coarse-Grained Level
Andras FiserAlbert Einstein College of MedicineHybrid protein structure modeling using Smotifs and NMR chemical shift information
Andriy KryshtafovychUniversity of CaliforniaNew Developments in the Assessment of Contact Predictions in CASP‚ and How to Quantify Improvements in Model Accuracy Due to Incorporation of Contact Information
Andrzej  JoachimiakArgonne National LaboratoryStructure Determination of Transcriptional Factors and their Complexes with DNA
Banu OzkanArizona State UniversityA novel protein structure refinement approach :Local Unfolding and Refolding
Bjorn WallnerLinkoping UniversityModel Quality Assessment and Refinement
Chandrajit BajajUniversity of TexasAutomated Prediction of Molecular Assemblies
Chen KeasarBen-Gurion UniversityScoring individual protein models by a purely structural function
Christopher JaroniecThe Ohio State UniversityStructural and Dynamic Studies of Protein Assemblies by Solid-State NMR Spectroscopy
Daisuke KiharaPurdue UniversityEvaluating Protein Structure Models by Considering Local Structural Contexts
Darrin M YorkRutgers UniversityPrediction of Active States of Protein and RNA Enzymes and the Role of pH and Ion Atmosphere on Structure and Catalysis
Dominik GrontUniversity of WarsawBioShell – Modular Platform For Biomolecular Modeling
Dong XuUniversity of MissouriDevelopment and Application of MUFOLD for Protein Structure Prediction
Drena DobbsIowa State UniversityAnalyzing & Predicting RNA-Protein Interactions 
Gabriel Del Rio GuerraUniversidad Nacional Autonoma de MexicoCorrect identification of functional sites in proteins for the prediction of protein structure
George StanUniversity of CincinnatiTopology-dependent mechanisms of protein unfolding and translocation by AAA+ nanomachines
Gregory ChirikjianJohns Hopkins UniversityAnalysis of Preferred Orientations of Interacting Substructures in Proteins 
Hamid  EghbalniaUniversity of CincinnatiBig Data Investigation of Proteins and RNA Molecules can Reveal Higher Order Heterogeneous Relationships 
Ilya VakserUniversity of KansasKnowledge-based modeling of protein-protein interactions
Ioan AndricioaeiUniversity of CaliforniaProtein and RNA Folding Exibits Universal Signatures of Granular Jamming
Jarek MellerUniversity of CincinnatiUltrafast Clustering of Macromolecular Structures
Jianlin ChengUniversity of MissouriAb Initio Prediction and Refinement of Protein Structures
Jie LiangUniversity of Illinois at ChicagoSampling and predicting conformations of single and multiple loops of proteins
Jim WangStony Brook UniversityQuantifying the Specificity of Ligand-Binding
Jinbo XuToyota Technological Institute at ChicagoA new protein statistical potential empowered by high-throughput sequencing
Joanna SulkowskaUniversity of WarsawTo Be Confirmed
Justin MacCallumStony Brook UniversityDetermining protein structures from sparse and unreliable data
Krzysztof FidelisUniversity of CaliforniaModeling protein structure with multi segment 3D motifs
Lukasz  KurganUniversity of AlbertaHigh-throughput prediction of protein-protein; protein-RNA and protein-DNA interactions mediated by disordered regions
Marek CieplakPolish Academy of ScienceEnergy landscape and dynamics of a lattice model of proteins
Michael FeigMichigan State UniversityProtein Structure Refinement using Molecular Dynamics Simulations
Nick GrishinUniversity of TexasEvolutionary Classification of Protein Domains
Olivier LichtargeBaylor College of MedicineA genotype to phenotype perturbation equation for the action of protein coding variations
Phil BradleyFred Hutchinson Cancer Research CenterPredicting protein-nucleic acid structures and interactions
Ralf BundschuhThe Ohio State UniversityRNA structure mediated cooperativity in RNA-protein interactions
Ram SamudralaUniversity of WashingtonComputational Analysis of Novel Drug Opportunities (CANDO)
Roland L. Dunbrack  JrFox Chase Cancer CenterStatistical Analysis of Protein Structures: Backbone Conformations‚ Side-Chain Rotamers Antibodies and Protein-Protein Interfaces
Ron ElberThe University of TexasPredicting the Structure of Protein Switches
Ross WalkerSan Diego Supercomputer CenterTowards and Automated Pipeline for the Refinement of RNA Crystal Structures
Ruxandra DimaUniversity of CincinnatiExploring structural diversity in proteins using single-molecule approaches
Samuel Flores Uppsala UniversityBackbone Flexibility is Key to Accurate and Reliable Evaluation of Mutations in Protein-Protein Interfaces
Sandor VajdaBoston UniversityWhat Docking tells us about Protein-protein Association
Shi-Jie ChenUniversity of MissouriPredicting Structure and Stability for RNA Complexes with Intermolecular Loop-loop Tertiary Contacts
Thomas E. Cheatham IIIUniversity of UtahUsing MD Simulation to Characterize the Structural Ensemble of RNA
William C. RayNationwide Children’s HospitalVisualizing Co-Evolution : What does Structure look like‚ and How can we tell it from Function? 
Wladek Minor University of VirginiaExperiment and Modeling: Competitive or Complementary Approaches to Structural Biology?
Xavier SalvatellaInstitute for Research in Biomedicine (IRB Barcelona)Implications of Order Disorder Transitions in the Androgen Receptor for the Onset and Treatment of Late Stage Prostate Cancer
Xiaoqin ZouUniversity of MissouriA scoring scheme for predicting protein structures

Contributing Speakers

Alberto Perez – Stony Brook University

Michael Deyholos – University of Alberta

Leon Martinez – Universidad Nacional Autonoma de Mexico

Faruck Morcos – Rice University

Annemarie Honegger – Zurich University

Dima Kozakov – Boston University

Andrei Korostelev – University of Massachusetts Medical School

Michael Widom – Carnegie Mellon University

Sebastian Kmiecik – University of Warsaw

Maksim Kouza – University of Warsaw

Peter Røgen – Technical University of Denmark

Cristina Cantale – ENEA

Falk Hoffmann – Research Centre Juelich

Joseph Dybas – Albert Einstein College of Medicine

Heping Zheng – University of Virginia

Jianzhu Ma – Toyota Technological Institute at Chicago

Brinda Vallat – Albert Einstein College of Medicine

Marcin Pawlowski – The Research Institute at Nationwide Children’s Hospital

Robert Pilstål – Linkoping University

Konstantinos Tsirigos – Stockholm University

Conference Programme

A copy of the conference programme can be viewed here Conference Programme

Conference Fees

StandardAccompanying Adult Accompanying Child (0-5 years)Accompanying Child (6-11 years)Extra Night AdultExtra Night Child (0-5 years)Extra Night Child (6-11 Years)
Day Pass $800
Payment Deadline Oct 30 Oct 30 Oct 30 Oct 30 Oct 30 Oct 30 Oct 30

Delegate Fees: Include conference registration and attendance, accommodation, all meals and drinks on a specially negotiated all-inclusive package and The Gala Night (including any accompanying persons).

Day Pass: includes conference registration and attendance, lunch and coffee breaks on conference days and The Gala Night. To register with a day pass please use the specified link below.

Accompanying Persons Fees: Include the same specially negotiated all-inclusive package as delegates excluding conference attendance.

Additional Night Fees: Prices are per person per night.

Conference Sponsors


Register Now For A Day Pass