Workshop
Machine Learning in Structural Biology Workshop
Hannah Wayment-Steele · Roshan Rao · Ellen Zhong · Sergey Ovchinnikov · Gabriele Corso · Gina El Nesr
Room 208 - 210
Fri 15 Dec, 6:30 a.m. PST
Structural biology, the study of the 3D structure or shape of proteins and other biomolecules, has been transformed by breakthroughs from machine learning algorithms. While methods such as AlphaFold2 have made exponential progress in certain areas, many active and open challenges for the field remain, including modeling protein dynamics, predicting the structure of other classes of biomolecules such as RNA, and ultimately relating the structure of isolated proteins to the in vivo and contextual nature of their underlying function. These challenges are diverse and require interdisciplinary collaboration between ML and structural biology researchers. The 4th edition of the Machine Learning in Structural Biology (MLSB) workshop focuses on these challenges and opportunities. In a unique commitment of support, PRX Life journal has committed to waiving publication fees for accepted papers in a special collection for interested authors. We anticipate this workshop will be of significant interest to both ML researchers as well as computational / experimental biologists and will stimulate continued problem-solving and new directions in the field.
Schedule
Fri 6:30 a.m. - 6:35 a.m.
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Opening Remarks
(
Remarks
)
>
SlidesLive Video |
🔗 |
Fri 6:35 a.m. - 7:00 a.m.
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Health system scale language models for clinical and operational decision making
(
Talk
)
>
SlidesLive Video |
Kyunghyun Cho 🔗 |
Fri 7:00 a.m. - 7:15 a.m.
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Validation of de novo designed water-soluble and membrane proteins by in silico folding and melting
(
Contributed
)
>
SlidesLive Video |
🔗 |
Fri 7:15 a.m. - 7:40 a.m.
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Accurate and tunable de novo protein shapes for new functions
(
Talk
)
>
SlidesLive Video |
Tanja Kortemme 🔗 |
Fri 8:00 a.m. - 8:25 a.m.
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A CryoET Data Portal to Foster a Collaboration between the Machine Learning and CryoET Communities
(
Talk
)
>
SlidesLive Video |
Bridget Carragher 🔗 |
Fri 8:25 a.m. - 8:40 a.m.
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AlphaFold Meets Flow Matching for Generating Protein Ensembles
(
Contributed
)
>
SlidesLive Video |
🔗 |
Fri 8:40 a.m. - 8:55 a.m.
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DSMBind: an unsupervised generative modeling framework for binding energy prediction
(
Contributed
)
>
SlidesLive Video |
🔗 |
Fri 8:55 a.m. - 9:20 a.m.
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Leveraging microfluidics for high-throughput and quantitative biochemistry and biophysics
(
Talk
)
>
SlidesLive Video |
Polly Fordyce 🔗 |
Fri 9:20 a.m. - 10:40 a.m.
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Poster Session 1/Lunch
(
Poster session
)
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🔗 |
Fri 10:40 a.m. - 11:05 a.m.
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Illuminating protein space with a programmable generative model
(
Talk
)
>
SlidesLive Video |
Gevorg Grigoryan 🔗 |
Fri 11:05 a.m. - 11:20 a.m.
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Protein generation with evolutionary diffusion: sequence is all you need
(
Contributed
)
>
SlidesLive Video |
🔗 |
Fri 11:20 a.m. - 11:45 a.m.
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De novo design of protein structure and function with RFdiffusion
(
Talk
)
>
SlidesLive Video |
Jason Yim · Brian L Trippe 🔗 |
Fri 12:00 p.m. - 12:15 p.m.
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DiffDock-Pocket: Diffusion for Pocket-Level Docking with Sidechain Flexibility
(
Contributed
)
>
SlidesLive Video |
🔗 |
Fri 12:15 p.m. - 12:30 p.m.
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PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses
(
Contributed
)
>
SlidesLive Video |
🔗 |
Fri 12:30 p.m. - 12:55 p.m.
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World-wide competitions and the RNA folding problem
(
Talk
)
>
SlidesLive Video |
Rhiju Das 🔗 |
Fri 1:00 p.m. - 2:00 p.m.
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Panel Session
(
Session
)
>
SlidesLive Video |
🔗 |
Fri 2:00 p.m. - 3:00 p.m.
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Poster Session 2 / Happy Hour
(
Poster Session
)
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🔗 |
Fri 3:00 p.m. - 3:05 p.m.
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Closing Remarks
(
Remarks
)
>
SlidesLive Video |
🔗 |
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ESMFold Hallucinates Native-Like Protein Sequences
(
Poster
)
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Jeliazko Jeliazkov · Diego del Alamo · Joel Karpiak 🔗 |
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Conditioned Protein Structure Prediction
(
Poster
)
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Tengyu Xie · Zilin Song · Jing Huang 🔗 |
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Stable Online and Offline Reinforcement Learning for Antibody CDRH3 Design
(
Poster
)
>
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Yannick Vogt · Mehdi Naouar · Maria Kalweit · Christoph Cornelius Miething · Justus Duyster · Roland Mertelsmann · Gabriel Kalweit · Joschka Boedecker 🔗 |
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Guiding diffusion models for antibody sequence and structure co-design with developability properties
(
Poster
)
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Amelia Villegas-Morcillo · Jana M. Weber · Marcel Reinders 🔗 |
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AlphaFold Distillation for Protein Design
(
Poster
)
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Igor Melnyk · Aurelie Lozano · Payel Das · Vijil Chenthamarakshan 🔗 |
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Binding Oracle: Fine-Tuning From Stability to Binding Free Energy
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Poster
)
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Chengyue Gong · Adam Klivans · Jordan Wells · James Loy · Qiang Liu · Alex Dimakis · Daniel Diaz 🔗 |
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Scalable Multimer Structure Prediction using Diffusion Models
(
Poster
)
>
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Peter Pao-Huang · Bowen Jing · Dr. Bonnie Berger 🔗 |
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Implicit Geometry and Interaction Embeddings Improve Few-Shot Molecular Property Prediction
(
Poster
)
>
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Christopher Fifty · Joseph M Paggi · Ehsan Amid · Jure Leskovec · Ron Dror 🔗 |
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Molecular Diffusion Models with Virtual Receptors
(
Poster
)
>
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Matan Halfon · Eyal Rozenberg · Ehud Rivlin · Daniel Freedman 🔗 |
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CESPED: a new benchmark for supervised particle pose estimation in Cryo-EM.
(
Poster
)
>
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Ruben Sanchez Garcia · Michael Saur · Javier Vargas · Carl Poelking · Charlotte Deane 🔗 |
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Learning Scalar Fields for Molecular Docking with Fast Fourier Transforms
(
Poster
)
>
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Bowen Jing · Tommi Jaakkola · Dr. Bonnie Berger 🔗 |
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VN-EGNN: Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification
(
Poster
)
>
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Florian Sestak · Lisa Schneckenreiter · Sepp Hochreiter · Andreas Mayr · Günter Klambauer 🔗 |
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Enhancing Ligand Pose Sampling for Machine Learning–Based Docking
(
Poster
)
>
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Patricia Suriana · Ron Dror 🔗 |
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Improved encoding of ensembles in PDBx/mmCIF
(
Poster
)
>
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Stephanie Wankowicz · James Fraser 🔗 |
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AlphaFold Meets Flow Matching for Generating Protein Ensembles
(
Poster
)
>
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Bowen Jing · Dr. Bonnie Berger · Tommi Jaakkola 🔗 |
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AlphaFold Meets Flow Matching for Generating Protein Ensembles
(
Oral
)
>
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Bowen Jing · Dr. Bonnie Berger · Tommi Jaakkola 🔗 |
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The Discovery of Binding Modes Requires Rethinking Docking Generalization
(
Poster
)
>
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Gabriele Corso · Arthur Deng · Nicholas Polizzi · Regina Barzilay · Tommi Jaakkola 🔗 |
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Conformational sampling and interpolation using language-based protein folding neural networks
(
Poster
)
>
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Diego del Alamo · Jeliazko Jeliazkov · Daphne Truan · Joel Karpiak 🔗 |
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FLIGHTED: Inferring Fitness Landscapes from Noisy High-Throughput Experimental Data
(
Poster
)
>
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Vikram Sundar · Boqiang Tu · Lindsey Guan · Kevin Esvelt 🔗 |
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Contrasting Sequence with Structure: \\Pre-training Graph Representations with PLMs
(
Poster
)
>
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Louis Robinson · Timothy Atkinson · Liviu Copoiu · Patrick Bordes · Thomas PIERROT · Thomas Barrett 🔗 |
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Target-Aware Variational Auto-Encoders for Ligand Generation with Multi-Modal Protein Modeling
(
Poster
)
>
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Khang Ngo · Truong Son Hy 🔗 |
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DSMBind: an unsupervised generative modeling framework for binding energy prediction
(
Poster
)
>
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Wengong Jin · Caroline Uhler · Nir HaCohen 🔗 |
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DSMBind: an unsupervised generative modeling framework for binding energy prediction
(
Oral
)
>
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Wengong Jin · Caroline Uhler · Nir HaCohen 🔗 |
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Fast non-autoregressive inverse folding with discrete diffusion
(
Poster
)
>
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John Yang · Jason Yim · Tommi Jaakkola · Regina Barzilay 🔗 |
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TopoDiff: Improve Protein Backbone Generation with Topology-aware Latent Encoding
(
Poster
)
>
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Yuyang Zhang · Zinnia Ma · Haipeng Gong 🔗 |
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Harmonic Prior Self-conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design
(
Poster
)
>
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Hannes Stärk · Bowen Jing · Regina Barzilay · Tommi Jaakkola 🔗 |
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CrysFormer: Protein Crystallography Prediction via 3d Patterson Maps and Partial Structure Attention
(
Poster
)
>
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Chen Dun · Tom Pan · Shikai Jin · Ria Stevens · Mitchell D. Miller · George Phillips · Anastasios Kyrillidis 🔗 |
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PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses
(
Poster
)
>
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Charles Harris · Kieran Didi · Arian Jamasb · Chaitanya Joshi · Simon Mathis · Pietro Lió · Tom Blundell 🔗 |
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PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses
(
Oral
)
>
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Charles Harris · Kieran Didi · Arian Jamasb · Chaitanya Joshi · Simon Mathis · Pietro Lió · Tom Blundell 🔗 |
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Sampling Protein Language Models for Functional Protein Design
(
Poster
)
>
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Jeremie Theddy Darmawan · Yarin Gal · Pascal Notin 🔗 |
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A framework for conditional diffusion modelling with applications in protein design
(
Poster
)
>
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Kieran Didi · Francisco Vargas · Simon Mathis · Vincent Dutordoir · Emile Mathieu · Urszula Julia Komorowska · Pietro Lió 🔗 |
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DiffRNAFold: Generating RNA Tertiary Structures with Latent Space Diffusion
(
Poster
)
>
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Mihir Bafna · Vikranth Keerthipati · Subhash Kanaparthi · Ruochi Zhang 🔗 |
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Pair-EGRET: Enhancing the prediction of protein-protein interaction sites through graph attention networks and protein language models
(
Poster
)
>
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Ramisa Alam · Sazan Mahbub · Md. Shamsuzzoha Bayzid 🔗 |
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FlexiDock: Compositional diffusion models for flexible molecular docking
(
Poster
)
>
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Zichen Wang · Balasubramaniam Srinivasan · Zhengyuan Shen · George Karypis · Huzefa Rangwala 🔗 |
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In vitro validated antibody design against multiple therapeutic antigens using generative inverse folding
(
Poster
)
>
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Amir Shanehsazzadeh 🔗 |
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Evaluating Zero-Shot Scoring for In Vitro Antibody Binding Prediction with Experimental Validation
(
Poster
)
>
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Divya Nori · Simon Mathis · Amir Shanehsazzadeh 🔗 |
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PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design
(
Poster
)
>
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Chuanrui WANG · Bozitao Zhong · Zuobai Zhang · Narendra Chaudhary · Sanchit Misra · Jian Tang 🔗 |
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Optimizing protein language models with Sentence Transformers
(
Poster
)
>
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Istvan Redl 🔗 |
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DiffDock-Pocket: Diffusion for Pocket-Level Docking with Sidechain Flexibility
(
Poster
)
>
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Michael Plainer · Marcella Toth · Simon Dobers · Hannes Stärk · Gabriele Corso · Céline Marquet · Regina Barzilay 🔗 |
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DiffDock-Pocket: Diffusion for Pocket-Level Docking with Sidechain Flexibility
(
Oral
)
>
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Michael Plainer · Marcella Toth · Simon Dobers · Hannes Stärk · Gabriele Corso · Céline Marquet · Regina Barzilay 🔗 |
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Transition Path Sampling with Boltzmann Generator-based MCMC Moves
(
Poster
)
>
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Michael Plainer · Hannes Stärk · Charlotte Bunne · Stephan Günnemann 🔗 |
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Pre-training Sequence, Structure, and Surface Features for Comprehensive Protein Representation Learning
(
Poster
)
>
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Youhan Lee · Hasun Yu · Jaemyung Lee · Jaehoon Kim 🔗 |
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Inpainting Protein Sequence and Structure with ProtFill
(
Poster
)
>
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Elizaveta Kozlova · Daniel Nakhaee-Zadeh Gutierrez · Arthur Valentin 🔗 |
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Investigating Protein-DNA Binding Energetic of Mismatched DNA
(
Poster
)
>
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Ruben Solozabal · Tamir Avioz · Yunxiang LI · Le Song · Martin Takac · Ariel Afek 🔗 |
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AntiFold: Improved antibody structure design using inverse folding
(
Poster
)
>
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Alissa M Hummer · Magnus H Høie · Tobias Olsen · Morten Nielsen · Charlotte Deane 🔗 |
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Improved B-cell epitope prediction using AlphaFold2 modeling and inverse folding latent representations
(
Poster
)
>
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Paolo Marcatili 🔗 |
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Combining Structure and Sequence for Superior Fitness Prediction
(
Poster
)
>
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Steffanie Paul · Pascal Notin · Aaron Kollasch · Debora Marks 🔗 |
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Epitope-specific antibody design using diffusion models on the latent space of ESM embeddings
(
Poster
)
>
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Tomer Cohen · Dina Schneidman 🔗 |
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Protein language models learn evolutionary statistics of interacting sequence motifs
(
Poster
)
>
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Zhidian Zhang · Hannah Wayment-Steele · Garyk Brixi · Matteo Dal Peraro · Dorothee Kern · Sergey Ovchinnikov 🔗 |
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Using artificial sequence coevolution to predict disulfide-rich peptide structures with experimental connectivity in AlphaFold
(
Poster
)
>
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Gabriella Gerlach · John Nicoludis 🔗 |
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Preferential Bayesian Optimisation for Protein Design with Ranking-Based Fitness Predictors
(
Poster
)
>
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Alex Hawkins-Hooker · Paul Duckworth · Oliver Bent 🔗 |
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FAFormer: Frame Averaging Transformer for Predicting Nucleic Acid-Protein Interactions
(
Poster
)
>
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Tinglin Huang · Zhenqiao Song · Rex Ying · Wengong Jin 🔗 |
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LightMHC: A Light Model for pMHC Structure Prediction with Graph Neural Networks
(
Poster
)
>
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12 presentersAntoine Delaunay · Yunguan Fu · Nikolai Gorbushin · Robert McHardy · Bachir Djermani · Liviu Copoiu · Michael Rooney · Maren Lang · Andrey Tovchigrechko · Ugur Sahin · Karim Beguir · Nicolas Lopez Carranza |
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FrameDiPT: SE(3) Diffusion Model for Protein Structure Inpainting
(
Poster
)
>
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15 presentersCheng ZHANG · Adam Leach · Thomas Makkink · Miguel Arbesú · Ibtissem Kadri · Daniel Luo · Liron Mizrahi · Sabrine Krichen · Maren Lang · Andrey Tovchigrechko · Nicolas Lopez Carranza · Ugur Sahin · Karim Beguir · Michael Rooney · Yunguan Fu |
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An Active Learning Framework for ML-Assisted Labeling of Cryo-EM Micrographs
(
Poster
)
>
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Robert Kiewisz · Tristan Bepler 🔗 |
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Validation of de novo designed water-soluble and membrane proteins by in silico folding and melting.
(
Poster
)
>
|
Alvaro Martin · Carolin Berner · Sergey Ovchinnikov · Anastassia Vorobieva 🔗 |
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Validation of de novo designed water-soluble and membrane proteins by in silico folding and melting.
(
Oral
)
>
|
Alvaro Martin · Carolin Berner · Sergey Ovchinnikov · Anastassia Vorobieva 🔗 |
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Structure, Surface and Interface Informed Protein Language Model
(
Poster
)
>
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Ioan Ieremie 🔗 |
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De Novo Short Linear Motif (SLiM) Discovery With AlphaFold-Multimer
(
Poster
)
>
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Theo Sternlieb · · Davian Ho · Jeffrey Chan 🔗 |
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AF2BIND: Predicting ligand-binding sites using the pair representation of AlphaFold2
(
Poster
)
>
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Artem Gazizov · Anna Lian · Casper Goverde · Sergey Ovchinnikov · Nicholas Polizzi 🔗 |
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Protein generation with evolutionary diffusion: sequence is all you need
(
Poster
)
>
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Sarah Alamdari · Nitya Thakkar · Rianne van den Berg · Alex X Lu · Nicolo Fusi · Ava Amini · Kevin Yang 🔗 |
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Protein generation with evolutionary diffusion: sequence is all you need
(
Oral
)
>
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Sarah Alamdari · Nitya Thakkar · Rianne van den Berg · Alex X Lu · Nicolo Fusi · Ava Amini · Kevin Yang 🔗 |
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Protein-Protein Docking with Latent Diffusion
(
Poster
)
>
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Matt McPartlon · Céline Marquet · Tomas Geffner · Daniel Kovtun · Alexander Goncearenco · Zachary Carpenter · Luca Naef · Michael Bronstein · Jinbo Xu 🔗 |
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HiFi-NN annotates the microbial dark matter with Enzyme Commission numbers
(
Poster
)
>
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Gavin Ayres 🔗 |
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Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion ( Poster ) > link | Alex Morehead · Jeffrey Ruffolo · Aadyot Bhatnagar · Ali Madani 🔗 |
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SO(3)-Equivariant Representation Learning in 2D Images
(
Poster
)
>
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Darnell Granberry · Alireza Nasiri · Jiayi Shou · Alex J. Noble · Tristan Bepler 🔗 |
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HelixDiff: Conditional Full-atom Design of Peptides With Diffusion Models
(
Poster
)
>
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Xuezhi Xie · Pedro A Valiente · Jisun Kim · Philip Kim 🔗 |
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DIFFMASIF: Score-Based Diffusion Models for Protein Surfaces
(
Poster
)
>
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14 presentersMehmet Akdel · Freyr Sverrisson · Dylan Abramson · Jean Feydy · Alexander Goncearenco · Yusuf Adeshina · Daniel Kovtun · Céline Marquet · Xuejin Zhang · David Baugher · Zachary Carpenter · Luca Naef · Michael Bronstein · Bruno Correia |
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FLAb: Benchmarking deep learning methods for antibody fitness prediction
(
Poster
)
>
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Michael F Chungyoun · Jeffrey Ruffolo · Jeffrey Gray 🔗 |
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Parameter-Efficient Fine Tuning of Protein Language Models Improves Prediction of Protein-Protein Interactions
(
Poster
)
>
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Samuel Sledzieski · Meghana Kshirsagar · Rahul Dodhia · Bonnie Berger · Juan Lavista Ferres 🔗 |
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TriFold: A New Architecture for Predicting Protein Sequences from Structural Data
(
Poster
)
>
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Harish Srinivasan · Jian Zhou 🔗 |
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End-to-End Sidechain Modeling in AlphaFold2: Attention May or May Not Be All That You Need
(
Poster
)
>
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Jonathan King · David Koes 🔗 |
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Coarse-graining via reparametrization avoids force-matching and back-mapping
(
Poster
)
>
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Nima Dehmamy · Csaba Both · Subhro Das · Tommi Jaakkola 🔗 |
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SE3Lig: SE(3)-equivariant CNNs for the reconstruction of cofactors and ligands in protein structures
(
Poster
)
>
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Guillaume Lamoureux · Sid Bhadra-Lobo · Anushriya Subedy · Sagar Khare 🔗 |
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Cramming Protein Language Model Training in 24 GPU Hours
(
Poster
)
>
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Nathan Frey · Taylor Joren · Aya Ismail · Allen Goodman · Stephen Ra · Kyunghyun Cho · Richard Bonneau · Vladimir Gligorijevic 🔗 |
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Preparation Of Labeled Cryo-ET Datasets For Training And Evaluation Of Machine Learning Models
(
Poster
)
>
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Aygul Ishemgulova · Alex J. Noble · Tristan Bepler · Alex De Marco 🔗 |
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EMPOT: partial alignment of density maps and rigid body fitting using unbalanced Gromov-Wasserstein divergence
(
Poster
)
>
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Aryan Tajmir Riahi · Chenwei Zhang · James Chen · Anne Condon · Khanh Dao Duc 🔗 |
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Fast protein backbone generation with SE(3) flow matching
(
Poster
)
>
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11 presentersJason Yim · Andrew Campbell · Yue Kwang Foong · Sarah Lewis · Victor Satorras · Michael Gastegger · Bas Veeling · Jose Jimenez-Luna · Regina Barzilay · Tommi Jaakkola · Frank Noe |
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Frame2seq: structure-conditioned masked language modeling for protein sequence design
(
Poster
)
>
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Deniz Akpinaroglu · Kosuke Seki · Eleanor Zhu · Tanja Kortemme 🔗 |
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Structure-Conditioned Generative Models for De Novo Ligand Generation: A Pharmacophore Assessment
(
Poster
)
>
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Shannon Smith · Leo Gendelev · Kangway Chuang · Seth Harris 🔗 |
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Jointly Embedding Protein Structures and Sequences through Residue Level Alignment
(
Poster
)
>
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Foster Birnbaum · Saachi Jain · Amy Keating · Aleksander Madry 🔗 |
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Evaluating Representation Learning on the Protein Structure Universe
(
Poster
)
>
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11 presentersArian Jamasb · Alex Morehead · Zuobai Zhang · Chaitanya K. Joshi · Kieran Didi · Simon Mathis · Charles Harris · Jian Tang · Jianlin Cheng · Pietro Lió · Tom Blundell |
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Enhancing Antibody Language Models with Structural Information
(
Poster
)
>
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Justin Barton · Jacob Galson · Jinwoo Leem 🔗 |
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Amortized Pose Estimation for X-Ray Single Particle Imaging
(
Poster
)
>
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Jay Shenoy · Axel Levy · Frederic Poitevin · Gordon Wetzstein 🔗 |
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Rethinking Performance Measures of RNA Secondary Structure Problems
(
Poster
)
>
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Frederic Runge · Jörg Franke · Daniel Fertmann · Frank Hutter 🔗 |
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Structure-based and leakage-free data splits for rigorous protein function evaluation
(
Poster
)
>
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Charlotte Rochereau · Mohammed AlQuraishi · Arthur Valentin · Gergo Nikolenyi 🔗 |
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Uncovering sequence diversity from a known protein structure
(
Poster
)
>
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Luca Alessandro Silva · Barthélémy Meynard · Carlo Lucibello · Christoph Feinauer 🔗 |
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Exploiting language models for protein discovery with latent walk-jump sampling
(
Poster
)
>
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Sai Pooja Mahajan · Nathan Frey · Dan Berenberg · Joseph Kleinhenz · Richard Bonneau · Vladimir Gligorijevic · Andrew Watkins · Saeed Saremi 🔗 |