Joint Integrative Computational Biology workshop and CAPRI Meeting

Contribution List

45. Integrative modeling meets deep learning: applications to crosslinking mass spectrometry

Dr Dina Schneidman (The Hebrew University of Jerusalem)

12/02/2024, 13:40

Talk

Computational Methods and Deep Learning

Recent progress in protein structure prediction significantly enhanced integrative structure modeling of large macromolecular assemblies by providing improved structural coverage for individual proteins and protein-protein interactions. However, direct prediction of large protein assemblies remains a challenge. I will introduce CombFold, a hierarchical and combinatorial assembly algorithm...

28. Analysis of protein-nucleic acid interactions in the PPI3D web server

Justas Dapkunas (Vilnius University)

12/02/2024, 14:05

Talk

Computational Methods and Deep Learning

To perform their functions, proteins frequently interact with other proteins and nucleic acids. Detailed information on these interactions can be obtained from the three-dimensional structures of the corresponding protein-protein or protein-nucleic acid complexes. Since the experimental structure determination is often tedious and expensive, computational structure prediction methods are...

17. Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

Dr Anila Sebastian (Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.)

12/02/2024, 14:30

Talk

Computational Methods and Deep Learning

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

Abstract
Glycosaminoglycans (GAGs) with repeating disaccharide units intricately engage with proteins, playing a crucial role in the spatial organization of the extracellular matrix and the transduction of biological signals in...

11. VTX: High-performance molecular structure and dynamics visualization

Matthieu Montes (Conservatoire National des Arts et Métiers)

12/02/2024, 14:55

Talk

Computational Methods and Deep Learning

Molecular visualization is a critical task usually performed by structural biologists and bioinformaticians to aid three processes that are essential in science and fundamental to understand structural molecular biology: synthesis, analysis and communication [1].
Here we present VTX, a molecular visualization software that includes a real-time high-performance molecular graphics engine...

46. Generating backbone conformational changes with seven league boots

Frederic Cazals (Inria)

12/02/2024, 15:50

Talk

Computational Methods and Deep Learning

Generating large amplitude conformational changes of complex biomolecules remains a challenge. This talk will review recent work on this problem, based on novel insights on loop closure techniques coupling kinematic models in dihedral angle spaces and MCMC sampling techniques of the Hit-and-Run type. Along the way, I will discuss connections with density of states calculations and...

4. Analysis of interfaces in protein complexes using Voronoi tessellations and graph neural networks

Dr Kliment Olechnovic (CNRS Laboratoire Jean Kuntzmann, Grenoble)

12/02/2024, 16:15

Talk

Computational Methods and Deep Learning

Given a molecular structure, it can be represented as a set of atomic balls, each ball having a van der Waals radius corresponding to the atom type. A ball can be assigned a region of space that contains all the points that are closer (or equally close) to that ball than to any other. Such a region is called a Voronoi cell and the partitioning of space into Voronoi cells is called Voronoi...

52. Complementarity based peptide docking and design

Alisa Khramushin (EPFL)

12/02/2024, 16:40

Talk

Computational Methods and Deep Learning

In recent years, computational protein engineering has become instrumental in developing drugs and therapies, especially with the rise of machine learning-based methods, that pushed the performance of such tools to a new level of accuracy. Despite the progress, such approaches still present limitations in terms of robustness and complexity of the design objectives they can accomplish. Two of...

54. Protein structure evolution and convergence

Mathilde Carpentier (SU - MNH - CNRS)

12/02/2024, 17:05

Talk

Computational Methods and Deep Learning

The number of known folds is limited to a few thousand and this number is surprisingly low, several orders of magnitude lower than the number of sequences in the biosphere. Biological or physical constraints may considerably limit the repertoire of folds. In this case, structural convergence should be frequent. However, several studies showed that distribution in proteomes may be a global...

3. Hybrid methods for analyzing conformational variability in cryo-EM and cryo-ET data

Dr Slavica Jonic (CNRS & Sorbonne University, Paris)

12/02/2024, 17:30

Talk

Computational Methods and Deep Learning

The elucidation of different conformations of biomolecular complexes is the key to understand the molecular mechanisms behind the biological functions of the complexes and the key to novel drug discovery. Single-particle cryo electron microscopy (cryo-EM) allows 3D reconstruction of multiple conformations of purified biomolecular complexes from their 2D images. Cryo electron tomography...

40. Generative models and analysis tools for the study of highly-flexible (intrinsically disordered) proteins

Juan Cortés (LAAS-CNRS)

13/02/2024, 08:10

Talk

Computational Methods and Deep Learning

Proteins can have very different architectures, generally involving a concatenation of relatively rigid domains and flexible regions. Indeed, many proteins in eukaryotes, prokaryotes and viruses are composed of several domains connected by linkers, and flexible tails are also frequently found at the termini of rigid domains. Besides, flexible loops connecting secondary structure elements...

44. Dissecting peripheral protein-membrane interfaces

Prof. Nathalie Reuter (University of Bergen)

13/02/2024, 08:35

Talk

Computational Methods and Deep Learning

Peripheral membrane proteins (PMPs) are soluble proteins that bind transiently to the surface of cell membranes. Having the ability to exist in both a soluble and a membrane-bound form their membrane-binding region is constrained to retain a fine balance of polar and hydrophobic character, which makes it difficult to distinguish it from the rest of their surface. As a result peripheral...

27. Spectral partitioning into protein structural domains

Edoardo Sarti (Inria)

13/02/2024, 09:00

Talk

Computational Methods and Deep Learning

The decomposition of a biomolecular complex into domains is an important step to investigate biological functions, and is also relevant to ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spectral clustering applied to a graph coding inter-atomic fluctuations derived from an elastic network model. We present a...

61. Integrative structure of a histone chaperone-histone complex

Hugo van Ingen (Utrecht University)

13/02/2024, 09:25

Talk

Computational Methods and Deep Learning

Histone chaperones play a crucial role in regulating the assembly and disassembly of chromatin. Our lab recently reported a novel chaperone binding mode in which histone chaperone APLF single-handedly assembled the histone complexes H2A-H2B and H3-H4 into the histone octamer. The chaperone domain of APLF consists of a short (~60 aa) intrinsically disordered, highly acidic domain (AD). As we...

42. Exploring the conformational space of proteins by enumeration in the frame of the Distance Geometry Problem

Therese Malliavin (Laboratoire de Physique et Chimie Theoriques)

13/02/2024, 10:20

Talk

Computational Methods and Deep Learning

The continuous development of the methods for the protein structure prediction was taking advantage from the precious experimental information obtained by structural biology as well as by sequencing of multiple organisms. Indeed, the general developed pipeline is based on determining conformations of protein fragments, and then using multiple sequence alignments to obtain long-range distances...

48. Integrative spatiotemporal map of nucleocytoplasmic transport

Barak Raveh (Hebrew University of Jerusalem)

13/02/2024, 10:45

Talk

Computational Methods and Deep Learning

The Nuclear Pore Complex (NPC) is one of the larger macromolecular complexes in eukaryotic cells. The NPC facilitates rapid and selective transport between the cytoplasm and the nucleus. Existing models of transport do not provide quantitative mechanistic explanations of how some key emergent properties such as the rapid transport rates of molecules as large as ribosomal units and viral...

62. Integrative modeling of protein oligomers using Heligeom

Chantal Prévost (CNRS et univ Paris Cité)

13/02/2024, 11:10

Talk

Computational Methods and Deep Learning

Protein oligomers can modify their overall architecture in response to changes in the environment, such as ion concentration and composition, the presence of small ligands or mechanic stress. These changes may involve small variations in the subunit-subunit interface which can lead to important changes in the overall shape due to multiplication effect. They may also involve large interface...

24. Asymmetric hydrophobic mismatch in assembly of ATP synthase rotor ring

Ivan Gushchin (Moscow Institute of Physics and Technology)

13/02/2024, 11:35

Talk

Computational Methods and Deep Learning

Rotary ATPases are multisubunit enzyme complexes that couple synthesis or hydrolysis of ATP molecules with transport of ions across a membrane. Their transmembrane part includes a homo- or a heterooligomer of c subunits called a c-ring, with a patch of several lipids confined inside it. Little is known about this patch; it is usually not well resolved in experimental structures, but it is...

39. Integrative ensemble modeling that utilizes distance distribution restraints

Gunnar Jeschke (ETH Zürich)

13/02/2024, 13:45

Talk

Protein conformational flexibility and solution experiments

AlphaFold2 predictions for the human proteome reveal that the great majority of all human proteins contain intrinsically disordered regions (IDRs) or do not cotnain a folded domain at all. The structure of such proteins must be represented by an ensemble of conformers. However, most experimental techniques provide ensemble-average restraints, which do not contain direct information on width of...

18. Mechanistic study of MexAB-OprM efflux pump by an integrative approach

Isabelle Broutin (université Paris Cité)

13/02/2024, 14:10

Talk

Protein conformational flexibility and solution experiments

Bacterial infections remain a major public concern due to the accelerated increase in the appearance of antibiotic resistance. Among the different mechanisms used by bacteria to resist to antibiotics, the active efflux plays a major role. In Gram-negative bacteria, this is achieved by tripartite efflux pumps that form a macromolecular assembly spanning both membranes of the cellular wall, the...

21. Challenges in visualizing structural flexibility of the SAGA complex

Gabor Papai (INSERM)

13/02/2024, 14:35

Talk

Protein conformational flexibility and solution experiments

Cryogenic electron microscopy (cryo-EM) stands out as a widely utilized technique for elucidating the structures of macromolecular proteins. This method involves capturing projections of protein specimens embedded in thin, amorphous ice, preserving them within the vacuum of an electron microscope. The resulting structure emerges from the averaging of thousands of particle images, revealing...

16. Deciphering protein conformational dynamics with cryo-EM and MD simulations

Rémi Vuillemot (LJK, Université Grenoble Alpes, France)

13/02/2024, 15:00

Talk

Protein conformational flexibility and solution experiments

Cryo-Electron Microscopy (cryo-EM) allows conformational studies of macromolecular complexes in their close-to-native state, essential for understanding their working mechanisms and for structure-based drug development. However, deciphering continuous conformational transitions of macromolecules, through the main cryo-EM processing techniques, Single Particle Analysis (SPA) and cryo-Electron...

47. Mariage of Cryo-EM, Solution Scattering, and Computational Science

Masaaki Sugiyama (Kyoto University, Institute for Integrated Radiation and Nuclear Science)

13/02/2024, 15:55

Talk

Protein conformational flexibility and solution experiments

Over the past five years, structural biology has undergone a significant progress. The Nobel Prize in Chemistry awarded in 2017 to the developers of cryo-electron microscopy (cryo-EM) marked a milestone, and the rapid progress and widespread adoption of this technique have demonstrated that the precise structural analysis of biomacromolecules is not limited to crystallography or solution...

9. Protein Dynamics at extreme Temperatures

Beatrice CAVIGLIA (Universite' Paris Cite', University of Perugia)

13/02/2024, 16:20

Talk

Protein conformational flexibility and solution experiments

Life has adapted to extreme conditions on Earth. One of the most striking evidences of adaptation to extreme environments are bacteria that are capable of thriving in a vast temperature range, from below 0° C in glacial waters to above 100° C in deep-sea hydrothermal vents. It is known that the individual molecular components of these organisms, exhibit enhanced stability and resistance to the...

32. POU5F1B and GOLPH3, two challenging proteins in structural biology

Dr Maria Marcaida (EPFL)

13/02/2024, 16:45

Talk

Protein conformational flexibility and solution experiments

During this seminar, two experimental structural biology projects will be discussed illustrating current challenges and limitations in the field. The first will show how sequence identity may fail in predicting the protein structure and function. The second deals with investigating protein-protein interactions experimentally with the aim of creating small molecule inhibitors that block such...

37. Integrative structural biology of cell extracts : an application to structurally undercharacterized organisms

Ambroise Desfosses (CNRS- IBS)

13/02/2024, 17:40

Talk

Protein conformational flexibility and solution experiments

Integrative structural biology of cell extracts bridges the gap between the high resolution structural characterisation of highly purified, isolated biomolecules and in situ electron tomography. This booming technique combines mass spectrometry (MS)-based proteomics and cryo-electron microscopy (cryo-EM) of fractionated cell extracts to quantitatively and structurally characterise endogenous...

10. Ensemble based calculations of spin-spin couplings in proteins: from ordered to disordered peptides

Amina Gaffour

13/02/2024, 18:05

Talk

Protein conformational flexibility and solution experiments

To acquire a better understanding of how proteins work at the molecular level, it is crucial to understand their structural characteristics. Various techniques have been developed to achieve this, such as computer-based methods for calculating and predicting NMR measurements including the spin-spin coupling constants (SSCCs). Multi-scale calculations combining molecular dynamics simulations...

23. Hinge disulfides in human IgG2 CD40 antibodies modulate receptor signaling by regulation of conformation and flexibility

Hayden FISHER (ESRF)

13/02/2024, 18:30

Talk

Protein conformational flexibility and solution experiments

The human IgG2 (hIgG2) isotype is unique in its ability to undergo redox based shuffling of its hinge disulfides. Previous work identified hIgG2 as the optimal isotype for mediating activation (agonism) of multiple tumour necrosis factor receptor superfamily (TNFRSF) members, with the hinge disulfides shown to be critical. CD40 is a co-stimulatory TNFRSF receptor that can be targeted using...

50. Intrinsically disordered regulators of endocytosis - an integrated NMR/single molecule fluorescence approach

Sigrid Milles (Forschungsverbund Berlin e.V. (FMP))

14/02/2024, 08:30

Talk

Protein conformational flexibility and solution experiments

Intrinsically disordered proteins (IDPs) lack clearly defined structure and are therefore highly flexible and easily adaptable to different binding partners. This makes them important players in many biological processes, often with vital regulatory functions. Their dynamic features and broad range of interaction modes, however, render them difficult to study and analyzing their complexes...

8. The Influence of Globular Domains on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation

Michael Bakker (Charles University)

14/02/2024, 08:55

Talk

Protein conformational flexibility and solution experiments

Unraveling the mysteries of Intrinsically Disordered Proteins (IDPs) and Regions (IDRs) is one of the greatest challenges in the 21st century. The flexibility of these regions allow proteins to adopt vastly different conformations, allowing them to facilitate the binding and unbinding of vital activation sites. These regions, even in well-studied proteins such as the tumor...

30. Integrative Biology to tackle mitochondrial respiration in Alzheimer’s pathogenesis

Montserrat Soler Lopez (ESRF)

14/02/2024, 09:20

Talk

Protein conformational flexibility and solution experiments

Respiratory complexes located in the internal membranes of our mitochondria are true macromolecular batteries: they couple the flow of electrons through clusters of metals and cofactors with a transfer of protons to create a gradient that provides the energy necessary for the ATP production and therefore to the nourishment of essential life processes. The first complex in the respiratory...

56. NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins involved in Viral Replication

martin blackledge

14/02/2024, 10:15

Talk

Protein conformational flexibility and solution experiments

Proteins are inherently dynamic, exhibiting conformational freedom on many timescales,[1] implicating structural rearrangements that play a major role in molecular interaction, thermodynamic stability and biological function. Intrinsically disordered proteins (IDPs) represent extreme examples where flexibility defines molecular function. In spite of the ubiquitous presence of IDPs throughout...

41. Structure and function relationships in protein homorepeats

Pau BERNADO (Centre de Biologie Structural (CBS-Montpellier))

14/02/2024, 10:40

Talk

Protein conformational flexibility and solution experiments

Homorepeats, repetitive sequences inserted in disordered proteins, play fundamental roles in biology and mutations in these low-complexity regions are linked to several neurodegenerative and developmental diseases. Despite their relevance, the structural characterization and modelling of these proteins remain challenging. From an experimental perspective, the severe signal overlap of their NMR...

38. Integrative structural biology with atomic force microscopy data

Jean-Luc Pellequer (IBS)

14/02/2024, 11:05

Talk

Protein conformational flexibility and solution experiments

Understanding the molecular and cellular function of biological molecules requires an accurate perception of their functional assemblies. The term "functional" refers to the actual structure of the bioactive molecule: it includes, but is not limited to, oligomerization, molecular partners, and their multiscale dynamics. Achieving such a functional goal requires a combination of techniques that...

57. CAPRI 2024: Pre- and post-Alphafold protein docking

Marc Lensink (CNRS)

14/02/2024, 14:15

Talk

CAPRI

55. Integrated pipeline for protein docking with extended and enhanced Alphafold-based modeling methods

Daisuke Kihara (Purdue University)

14/02/2024, 15:00

Talk

CAPRI

Our group, Kiharalab, participated in both the prediction and scoring stages for complex targets. We combined three components in our pipeline, DistPepFold [1], AFSample [2], and a consensus-based score called ranksum we developed for our LZerD protein docking program [3]. For peptide docking, we used our new approach, DistPepFold. DistPepFold improves protein-peptide complex docking using an...

36. Towards integrative use of pyDock and AI-based modeling in 8th CAPRI

Juan Fernandez-Recio (ICVV-CSIC and BSC)

14/02/2024, 16:15

Talk

CAPRI

We have participated, both as predictors and as scorers, in all proposed targets of the 8th CAPRI edition. Here we will focus on the 11 purely CAPRI targets, that is, excluding the CASP-CAPRI joint rounds 46, 50 and 54, already evaluated and discussed in the respective CASP meetings, and the 4 targets in round 51 related to COVID19, with no available structure for evaluation. These 11 targets...

35. Prediction and refinement of protein assemblies with ClusPro, Alphafold and Molecular Dynamics.

Dima Kozakov (Stony Brook University)

14/02/2024, 16:45

Talk

CAPRI

In the latest CAPRI round our group used a combination of Alphafold-Multimer (AFM), the ClusPro webserver for docking, and Molecular Dynamics based sampling to refine models for small targets. Assembly prediction was based on a two-stage methodology, in which we first generate an ensemble of initial models using AlphaFold-Multimer using standard protocol for MSA generation. We stop the...

19. MassiveFold: optimized massive sampling with AlphaFold2

Guillaume Brysbaert (CNRS University of Lille)

14/02/2024, 17:15

Talk

CAPRI

Massive sampling with AlphaFold-multimer(1,2) showed impressive results for structural prediction of macromolecular assemblies at CASP15-CAPRI(3). Generating a very large number of predictions (>1000) and pushing their diversity by playing with the neural network model versions, the number of recycle steps, the use of templates or not and the activation of the dropout in the Evoformer and in...

63. From Interaction Prediction to Sequence Design: Unveiling PeSTo's Potential in Structural Biology

Lucien Krapp (Laboratory for Biomolecular Modeling, EPFL)

14/02/2024, 17:45

Talk

CAPRI

In the field of structural biology, predicting protein interactions and designing sequences based on backbone scaffolds remain pivotal yet challenging tasks. Built on the same deep learning architectural framework, Protein Structure Transformer (PeSTo) and its derivative, CARBonAra, address these challenges. PeSTo employs geometric transformers to proficiently predict diverse protein binding...

12. Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: The CASP Perspective

Ezgi Karaca (Izmir Biomedicine and Genome Center, DEU)

15/02/2024, 09:00

Talk

CAPRI

In CASP15, 87 predictors submitted around 11,000 models on 41 assembly targets. The community demonstrated exceptional performance in overall fold and interface contact prediction, achieving an impressive success rate of 90% (compared to 31% in CASP14). This remarkable accomplishment is largely due to the incorporation of DeepMind’s AF2-Multimer approach into custom-built prediction pipelines....

51. What have we learned (and memorized) about peptide-mediated interactions in CAPRI and beyond?

Ora Schueler-Furman (Hebrew University of Jerusalem)

15/02/2024, 09:30

Talk

CAPRI

Since the last CAPRI meeting, much has happened in the modeling field. Deep Learning (DL) has revolutionized structure prediction, and we are only beginning to grasp the fruits, as well as the new challenges uncovered in this new era.
I will describe different approaches that we developed and applied to address CAPRI challenges, and how they helped us shape and improve our ability to model,...

31. HADDOCK in latest CAPRI rounds

Dr Marco Giulini (Utrecht University), Dr Victor Reys (Utrecht University)

15/02/2024, 10:00

Talk

CAPRI

The HADDOCK team have participated as human and webserver predictor and/or scorer in last CAPRI rounds (47-55), mainly relying on the use of our integrative modelling software HADDOCK[1] which is able to use user-provided information to guide the docking process. An important element of HADDOCK is its scoring function, computed from the weighted sum of 4 energetical terms (VdW, Electrostatics,...

53. Assessing the impact of single-point mutations and alternative splicing-induced variations on protein-protein interactions

Elodie Laine

15/02/2024, 11:00

Talk

CAPRI

Beyond determining the 3D arrangement of interacting protein partners, assessing the impact of sequence variations on binding affinity and specificity is of utmost importance. I will present two methods we developed to address this question. The first method, DLA-Mutation [1], relies on geometric deep learning for predicting mutation-induced binding affinity changes. It exploits and contrasts...

58. The Expanding Horizon of Protein Interactions

Shoshana Wodak (VIB-VUB Center doe Structural Biooogy, Brussels Belgium)

15/02/2024, 11:30

Talk

CAPRI

20. Multistage Docking Approach for Protein-RNA Interactions Prediction in CAPRI and CASP

Shan Chang (Jiangsu University of Technology)

15/02/2024, 14:00

Talk

CAPRI

Protein-RNA interactions and recognition are essential in gene expression, regulation of transcription, and other biological processes. Prediction of protein and RNA is also a new challenge category for CAPRI and CASP. In this work, we proposed a multistage docking protocol called CoDockPR, which integrates the shape complementarity, knowledge-based scoring functions, and interface similarity...

26. An Iteratively Derived Knowledge-based Scoring Function at Atomic Level for Protein-DNA Complexes Evaluations

XIaoqin Zou (University of Missouri - Columbia)

15/02/2024, 14:30

Talk

CAPRI

Protein-DNA interactions play a significant role in biological processes and drug design owing to their prevalence. Computational methods for predicting protein-DNA complex structures serve as a valuable alternative to experimental methods, which, although more accurate, are also time-consuming and resource-intensive. The established framework for predicting protein-protein complex structures...

29. FTDMP: a framework for protein-protein, protein-DNA and protein-RNA docking and scoring

Rita Banciul (Vilnius University), Justas Dapkunas (Vilnius University)

15/02/2024, 15:00

Talk

CAPRI

Understanding the functions of protein-protein and protein-nucleic acid complexes relies on the knowledge of their 3D structures that can either be solved experimentally or predicted computationally. While AlphaFold has revolutionized protein structure prediction, challenges remain, particularly in modeling antibody-antigen interactions, protein-nucleic acid complexes, and proteins lacking...

49. Interpretable Affinity Prediction and Generative Design for Protein-Ligand Interactions

Yang Shen (Texas A&M University)

15/02/2024, 16:15

Talk

CAPRI

In this talk I will introduce our recent works on machine learning for protein-ligand interactions, including explainable prediction of protein-ligand binding affinity and structure-based de novo ligand design.

First, as deep learning methods for modeling protein-ligand interactions are increasingly improving their accuracy, their interpretability is often under-explored. We had...

59. Automated protein-to-Structure pipelines for new structures and X-ray based ligand screening at EMBL Grenoble. Experience from our first collaboration with CAPRI

José Márquez (EMBL Grenoble)

15/02/2024, 16:45

Talk

CAPRI

13. Shape retrieval methods for the classification of protein surfaces

Grisell Diaz Leines (EMBL-EBI)

16/02/2024, 09:00

Talk

CAPRI

Macromolecular complexes play a crucial role in almost all biological functions in living cells. Elucidating structural features in proteins is essential to understanding their underlying functions and binding activity. With the rapid accumulation of protein-structure data through AI methods and experimental techniques, such as cryo-electron microscopy, there is a growing demand for efficient...

25. High-throughput prediction of ATP synthase rotor ring stoichiometries

Ivan Gushchin (Moscow Institute of Physics and Technology)

16/02/2024, 09:30

Talk

CAPRI

Rotary ATP synthases are large enzyme complexes present in every living cell. They consist of a transmembrane and a soluble domain, each comprising multiple subunits. The transmembrane part contains an oligomeric rotor ring (c-ring), whose stoichiometry defines the ratio between the number of synthesized ATP molecules and the number of ions transported through the membrane. Here, we present...

5. Unsupervised Machine Learning and Phase Space Reduction: A Robust and Generalisable Approach for Concurrently Solving the Protein Complex Conformation Classification and Quantification Problems.

Dr Daniel Celis Garza (CCP4, Research Complex at Harwell, STFC Rutherford-Appleton Laboratory, UK)

16/02/2024, 10:30

Talk

CAPRI

The understanding of biochemical processes and the machinery of life hinges on comprehending the structural aspects of macromolecular interactions. This requires a systematic approach to analysing the vast manifold of macromolecular associations, or complexes, typically determined from crystallographic or electron microscopy experiments. Specific points of interest include similarity...

34. Modeling of immune recognition and protein complexes with deep learning and physics-based docking

Brian Pierce (University of Maryland)

16/02/2024, 11:00

Talk

CAPRI

The Pierce group has utilized a combination of AlphaFold and traditional docking methods, including Rosetta and ZDOCK, to model protein complexes in recent CAPRI and CASP/CAPRI rounds. This has led to success for several challenging targets, as well as useful lessons learned for prospective modeling efforts. Our group has been particularly focused on the utilization and adaptation of AlphaFold...

6. A new approach for assigning names and persistent, unique identifiers to macromolecular complexes in the Protein Data Bank

Sri Appasamy (Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI))

Poster

Macromolecular complexes are key functional components in nearly all biological processes, and achieving an atomic-level understanding of them is crucial for unravelling their molecular mechanisms. The Protein Data Bank (PDB) is the primary worldwide repository of experimentally determined macromolecular structures, offering valuable insights into the dynamics, conformations, and functional...

7. Computational Design of Peptides as Detectors, Drugs and Biomaterials

Sudeep Sarma (Johns Hopkins University)

Poster

Computational design of peptides that can (a) recognize/bind to specific protein interfaces and (b) self-assemble into nano-scale architectures such as β-sheet-based fibrils (amyloid) have potential applications in healthcare and advanced biomaterial fabrication. Screening sequence space via experiments to discover peptides that bind to proteins and self-assemble is challenging, although some...

14. Deep Learning in Protein Docking: Discriminative vs. Generative Models

Mr Lee-Shin Chu (Johns Hopkins University)

Poster

Traditional protein-protein docking algorithms often rely on extensive candidate sampling and subsequent re-ranking. However, these steps are time-consuming, limiting their applicability in scenarios requiring high-throughput complex structure prediction, such as structure-based virtual screening. The advent of deep learning methods has brought acceleration to the docking process, leveraging...

22. Detailed analysis of a thermostable protein-DNA complex: the case of Sac7d as a prototype for protein-DNA interaction

Elena Alvarez Sanchez (Nantes Université, US2B, CNRS, UMR6286 & Affilogic, Nantes, France)

Poster

Sac7d is a 7kDa protein belonging to the class of the small chromosomal proteins
from archeon Sulfolobus acidocaldarius. Sac7d was discovered in 1974 in Yellowtone
National Parks geysers, and studied extensively since then for its remarkable
stability at large pH and temperature ranges. Sac7d binds to DNA minor groove to
protect DNA from these extreme conditions by increasing its melting...

43. Integrative structural biology of cell extracts : a Blob case study

Ambroise Desfosses (CNRS-IBS)

Poster

Integrative structural biology of cell extracts bridges the gap between the high resolution structural characterisation of highly purified, isolated biomolecules and in situ electron tomography. This booming technique combines mass spectrometry (MS)-based proteomics and cryo-electron microscopy (cryo-EM) of fractionated cell extracts to quantitatively and structurally characterise endogenous...