mlsanityData to 14 Oct 2026

SurfPro: Functional Protein Design Based on Continuous Surface

arXiv 2405.06693 ↗First posted 7 May 2024q-bio.BM cs.LGcited by 14

Not on the map. Why?

Abstract (arXiv)

How can we design proteins with desired functions? We are motivated by a chemical intuition that both geometric structure and biochemical properties are critical to a protein's function. In this paper, we propose SurfPro, a new method to generate functional proteins given a desired surface and its associated biochemical properties. SurfPro comprises a hierarchical encoder that progressively models the geometric shape and biochemical features of a protein surface, and an autoregressive decoder to produce an amino acid sequence. We evaluate SurfPro on a standard inverse folding benchmark CATH 4.2 and two functional protein design tasks: protein binder design and enzyme design. Our SurfPro consistently surpasses previous state-of-the-art inverse folding methods, achieving a recovery rate of 57.78% on CATH 4.2 and higher success rates in terms of protein-protein binding and enzyme-substrate interaction scores.

Key facts. Cited by 14 papers in the map (data through 14 Oct 2026). Builds on 15 of its 53 references that are in the map. First posted on arXiv 7 May 2024.

Builds on

15 of 53 references.

References · 15

  1. 2017Attention Is All You Needcited by 60,361
  2. 2021E(n) Equivariant Graph Neural Networkscited by 965
  3. 2017Sigmoid-Weighted Linear Units for Neural Network Function Approximation in Reinforcement Learningcited by 950
  4. 2020Learning from Protein Structure with Geometric Vector Perceptronscited by 313
  5. 2022Biological Sequence Design with GFlowNetscited by 174
  6. 2021Frame Averaging for Invariant and Equivariant Network Designcited by 168
  7. 2019Conditioning by adaptive sampling for robust designcited by 111
  8. 2020Glancing Transformer for Non-Autoregressive Neural Machine Translationcited by 103
  9. 2020Fully Non-autoregressive Neural Machine Translation: Tricks of the Tradecited by 99
  10. 2019Model Inversion Networks for Model-Based Optimizationcited by 83
  11. 2022PiFold: Toward effective and efficient protein inverse foldingcited by 83
  12. 2023Structure-informed Language Models Are Protein Designerscited by 68
3 more
  1. 2018Design by adaptive samplingcited by 32
  2. 2023Importance Weighted Expectation-Maximization for Protein Sequence Designcited by 12
  3. 2021Voxel Structure-based Mesh Reconstruction from a 3D Point Cloudcited by 7

Built on by

Cited by year (2026 to 14 Oct)

Citing papers per year: 2025: 9; 2026: 5.

14 papers.

Sort:

  1. 2025All-atom inverse protein folding through discrete flow matchingcited by 8
  2. 2025PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representationscited by 6
  3. 2025Tokenizing Electron Cloud in Protein-Ligand Interaction Learningcited by 3
  4. 2025PPDiff: Diffusing in Hybrid Sequence-Structure Space for Protein-Protein Complex Designcited by 3
  5. 2026Surface-based Molecular Design with Multi-modal Flow Matchingcited by 3
  6. 2026Property-driven Protein Inverse Folding With Multi-Objective Preference Alignmentcited by 3
  7. 2026AbFlow : End-to-end Paratope-Centric Antibody Design by Interaction Enhanced Flow Matchingcited by 2
  8. 2025EnzyControl: Adding Functional and Substrate-Specific Control for Enzyme Backbone Generationcited by 1
  9. 2025DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Designcited by 0
  10. 2025AlphaFold Database Debiasing for Robust Inverse Foldingcited by 0
  11. 2025SculptDrug : A Spatial Condition-Aware Bayesian Flow Model for Structure-based Drug Designcited by 0
  12. 2025Joint Design of Protein Surface and Structure Using a Diffusion Bridge Modelcited by 0
2 more
  1. 2026From Snapshots to Symphonies: The Evolution of Protein Prediction from Static Structures to Generative Dynamics and Multimodal Interactionscited by 0
  2. 2026SurfDesign: Effective Protein Design on Molecular Surfacescited by 0