マップ 1
protein
  structure
    prediction
      general
        review
          Uncovering protein structure
          Protein Structure Prediction: Conventional and Deep Learning Perspectives
          De novo peptide structure prediction: an overview
          Protein structural motifs in prediction and design
        physics
          I-TASSER: a unified platform for automated protein structure and function prediction
          Foldit
            Predicting protein structures with a multiplayer online game
        MD simulation
          Molecular Dynamics Simulation for All
        deep learning
          review
            Deep Learning-Based Advances in Protein Structure Prediction
            Deep Learning in Protein Structural Modeling and Design
          solvent accessible
            Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method
            DeepREx-WS: A web server for characterising protein-solvent interaction starting from sequence
          Improved protein structure prediction using predicted interresidue orientations
          ColabFold: making protein folding accessible to all
      antibody
        review
          VHH Structural Modelling Approaches: A Critical Review
        descriptor
          Quantitative Description of Surface Complementarity of Antibody-Antigen Interfaces
        Antibody side chain conformations are position-dependent
        deep learning
          Differential performance of RoseTTAFold in antibody modeling
          Simple End-to-end Deep Learning Model for CDR-H3 Loop Structure Prediction
          Antibody structure prediction using interpretable deep learning
          Geometric potentials from deep learning improve prediction of CDR H3 loop structures
      loop
        review
          Computational design of structured loops for new protein functions
          Current approaches to flexible loop modeling
      unit/motif
        review
          Basic units of protein structure, folding, and function
          Protein three-dimensional structures at the origin of life
        TERMs
          Tertiary alphabet for the observable protein structural universe
        SCHEMA
          Protein building blocks preserved by recombination
        Closed loop
          Closed loops of nearly standard size: common basic element of protein structure
          Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure
        Smotif
          A modular perspective of protein structures: application to fragment based loop modeling
          Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures
        nest
          A novel main-chain anion-binding site in proteins: the nest. A particular combination of phi,psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions
        modulality
          Quantifying protein modularity and evolvability: a comparison of different techniques
        hydrophobic folding unit
          Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape
    docking
      reivew
        What method to use for protein-protein docking?
        Information-driven modeling of biomolecular complexes
        In silico Approaches for the Design and Optimization of Interfering Peptides Against Protein-Protein Interactions
      general
        deep learning
          ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction
          Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
          SSnet: A Deep Learning Approach for Protein-Ligand Interaction Prediction
      antibody
        benchmark
          An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants
        information-driven
          Modeling Antibody-Antigen Complexes by Information-Driven Docking
          Functional antibody characterization via direct structural analysis and information-driven protein-protein docking
        deep learning
          embedding
            A compact vocabulary of paratope-epitope interactions enables predictability of antibody antigen binding
          PointNet
            Protein interaction interface region prediction by geometric deep learning
          GAN
            Learning context-aware structural representations to predict antigen and antibody binding interfaces
    clustering
      parametric
        A ‘periodic table’ for protein structures
        De novo protein design: how do we expand into the universe of possible protein structures?
      DPAM: A Domain Parser for AlphaFold Models
    tool
      Rosetta
        review
          Macromolecular modeling and design in Rosetta: recent methods and frameworks
        Prediction
          energy function
            The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
            Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules
          Protein structure prediction using Rosetta
          loop modeling
            CCD
              Cyclic coordinate descent: A robotics algorithm for protein loop closure
            KIC
              Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
        Design
          review
            Essentials of de novo protein design: Methods and applications
          RosettaRemodel: a generalized framework for flexible backbone protein design
          Motif-Driven Design of Protein-Protein Interfaces
          Proof of principle for epitope-focused vaccine design
          Rosetta FunFolDes – A general framework for the computational design of functional proteins
          Designing Peptides on a Quantum Computer
        Interface
          PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
          PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design
      structure embedding
        GNN
          Graphein – a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures and Interaction Networks
  design
    review
      Computational design of novel protein-protein interactions - An overview on methodological approaches and applications
      Increasing computational protein design literacy through cohort-based learning for undergraduate students
      Arming Yourself for The In Silico Protein Design Revolution
      history
        De novo protein design, a retrospective
        A Brief History of De Novo Protein Design: Minimal, Rational, and Computational
      minimal protein design
        Protein design, a minimalist approach
      rational protein design
        Designing artificial enzymes by intuition and computation
      deep learning
        Deep learning techniques have significantly impacted protein structure prediction and protein design
        Protein design via deep learning
        From sequence to function through structure: deep learning for protein design
      multi-state
        Deep learning approaches for conformational flexibility and switching properties in protein design
    sequence design
      general
        structure to
          Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design
          Protein sequence design with a learned potential
          Protein sequence design by conformational landscape optimization
          Robust deep learning based protein sequence design using ProteinMPNN
          ProteinSolver
            Fast and Flexible Protein Design Using Deep Graph Neural Networks
            Computational generation of proteins with predetermined three-dimensional shapes using ProteinSolver
            Designing novel protein structures using sequence generator and AlphaFold2
        language model
          A deep unsupervised language model for protein design
          Evaluating Protein Transfer Learning with TAPE
      antibody
        language model
          Generative Language Modeling for Antibody Design
          ImmunoLingo: Linguistics-based formalization of the antibody language
          On Pre-training Language Model for Antibody
          Multi-segment preserving sampling for deep manifold sampler
    structure design
      general
        β-barrel
          De novo design of a fluorescence-activating β-barrel
        HLH
          parametric
            Exploring the repeat protein universe through computational protein design
        minimal protein design
          De novo design of helical bundles as models for understanding protein folding and function
        model-based
          Using AlphaFold for Rapid and Accurate Fixed Backbone Protein Design
          AlphaDesign: A de novo protein design framework based on AlphaFold
          De novo protein design by deep network hallucination
          Scaffolding protein functional sites using deep learning
        GNN
          Neural Network-Derived Potts Models for Structure-Based Protein Design using Backbone Atomic Coordinates and Tertiary Motifs
          Generative models for graph-based protein design
          Learning from Protein Structure with Geometric Vector Perceptrons
          XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers
        Diffusion
          Illuminating protein space with a programmable generative model
          ProteinSGM: Score-based generative modeling for de novo protein design
          Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models
    function
      binder
        interface
          general
            dock＆optimize
              parametric
                De novo design of modular peptide binding proteins by superhelical matching
              physics
                Massively parallel de novo protein design for targeted therapeutics
                RIF docking
                  Design of protein binding proteins from target structure alone
                  De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
            hot-spot centric
              physics
                TERM
                  Tertiary motifs as building blocks for the design of protein-binding peptides
                  A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures
                van der Mer
                  A defined structural unit enables de novo design of small-molecule-binding proteins
            deep leaning
              CNN
                De novo design of site-specific protein interactions with learned surface fingerprints
              LSTM
                One-sided design of protein-protein interaction motifs using deep learning
              Diffusion
                Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models
                De novo design of high-affinity protein binders to bioactive helical peptides
            optimization
              Now What Sequence? Pre-trained Ensembles for Bayesian Optimization of Protein Sequences
              Language models enable zero-shot prediction of the effects of mutations on protein function
          antibody
            review
              Computational approaches to therapeutic antibody design: established methods and emerging trends
            physics
              AbDesign
                AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences
                Principles for computational design of binding antibodies
              OptMAV
                OptMAVEn-2.0: De novo Design of Variable Antibody Regions against Targeted Antigen Epitopes
                Computational de novo design of antibodies binding to a peptide with high affinity
                De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)
              RAbD
                RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
              CDR grafting
                Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences
                Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping
            deep learning
              review
                Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies
              CNN
                DLAB-Deep learning methods for structure-based virtual screening of antibodies
              LSTM
                In silico proof of principle of machine learning-based antibody design at unconstrained scale
              Transformer
                Accelerating Antibody Design with Active Learning
              VAE
                Deep Generative Design of Epitope-Specific Binding Proteins by Latent Conformation Optimization
              GNN
                Conditional Antibody Design as 3D Equivariant Graph Translation
                Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design
              Diffusion
                Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures
            optimization
              AntBO: Towards Real-World Automated Antibody Design with Combinatorial Bayesian Optimisation
              RL
                Structured Q-learning For Antibody Design
            screening data driven
              Predicting antibody binders and generating synthetic antibodies using deep learning
              Computational counterselection identifies nonspecific therapeutic biologic candidates
              Antibody Representation Learning for Drug Discovery
        scaffold
          Outpainting
            Computational Design of Potential Binder Protein for SARS-CoV-2 Spike RBD through A Novel Deep Neural Network Based-Protein Outpainting Algorithm
          antibody
            hallucination
              Hallucinating structure-conditioned antibody libraries for target-specific binders
            VAE
              End-to-End deep structure generative model for protein design
              Ig-VAE: Generative Modeling of Protein Structure by Direct 3D Coordinate Generation
            transformer
              BioPhi: A platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning
            AR
              Protein design and variant prediction using autoregressive generative models
            GNN
              Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design
              Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement
        filtration
          Improving de novo Protein Binder Design with Deep Learning
      vaccine
        dock＆optimize
          De novo protein design enables the precise induction of RSV-neutralizing antibodies
      function as text
        Automated Protein Function Description for Novel Class Discovery
  informatics
    quantum computing
      The prospects of quantum computing in computational molecular biology
  gene
    plasmid vector
      The art of vector engineering: towards the construction of next-generation genetic tools
    plasmid construction
      review
        DNA Assembly Tools and Strategies for the Generation of Plasmids
        In vivo DNA assembly using common laboratory bacteria: A re-emerging tool to simplify molecular cloning
      Recombinant DNA technologies for construction of precisely designed transgene constructs
    virus vector
      New developments in lentiviral vector design, production and purification
    mutagenesis
      Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells
      Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis
      CRISPR
        Programmable base editing of A・T to G・C in genomic DNA without DNA cleavage
        CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window
        Web-based design and analysis tools for CRISPR base editing
  preparation
    codon
      Computational tools and algorithms for designing customized synthetic genes
      COSMO: A dynamic programming algorithm for multicriteria codon optimization
    cell free
      High-throughput screening of biomolecules using cell-free gene expression systems
      Cell-free platforms for flexible expression and screening of enzymes
      Cell-free translation systems for protein engineering
      Effective Use of Linear DNA in Cell-Free Expression Systems
  engineering
    dimerizer
      FKBP Ligands-Where We Are and Where to Go?
  antibody
    screening
      Animal Immunization, in Vitro Display Technologies, and Machine Learning for Antibody Discovery
      Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design
      Predicting Antibody Developability Profiles Through Early Stage Discovery Screening
      Boosting antibody developability through rational sequence optimization
    clustering
      A new clustering of antibody CDR loop conformations
    epitope
      Antibody Specific B-Cell Epitope Predictions: Leveraging Information From Antibody-Antigen Protein Complexes
  enzyme
    Cell-free Directed Evolution of a Protease in Microdroplets at Ultrahigh Throughput
    Ultra-high throughput screening for novel protease specificities
    In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity
    Droplet Microfluidics-Enabled High-Throughput Screening for Protein Engineering
  peptide
    AlphaFold encodes the principles to identify high affinity peptide binders
  screening
    review
      Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases
    display system
      High-throughput characterization of protein-protein interactions by reprogramming yeast mating
    anti-virus
      VDDB: a comprehensive resource and machine learning platform for antiviral drug discovery
  cell therapy
    HSC trasplantation
      review
        Antibody based conditioning for allogeneic hematopoietic stem cell transplantation
        Allogeneic hematopoietic stem cell transplantation: lessons learned by a molecular immunologist/transplant patient
        Umbilical cord blood: an undervalued and underutilized resource in allogeneic hematopoietic stem cell transplant and novel cell therapy applications
    CAR-T
      review
        A Review of Clinical Outcomes of CAR T-Cell Therapies for B-Acute Lymphoblastic Leukemia
        Chimeric Antigen Receptor T Cell Therapy versus Hematopoietic Stem Cell Transplantation: An Evolving Perspective
    blood cancer
      review
        Acute lymphoblastic leukaemia
  signaling
    circuit
      review
        Programmable protein circuit design
      Notch
        Engineering of an enhanced synthetic Notch receptor by reducing ligand-independent activation
        The Role of Intracellular Trafficking of Notch Receptors in Ligand-Independent Notch Activation
        Selective use of ADAM10 and ADAM17 in activation of Notch1 signaling
      transcription factor
        Reprogramming cell fate with artificial transcription factors
        Regulation of transcription factor function by phosphorylation
        STAT
          Dynamics and non-canonical aspects of JAK/STAT signalling
          Tracking STAT nuclear traffic
          Crystal Structure of a Tyrosine Phosphorylated STAT-1 Dimer Bound to DNA
      nuclear transport
        Importin α : functions as a nuclear transport factor and beyond
        Molecular basis for specificity of nuclear import and prediction of nuclear localization
    receptor
      Comprehensive binary interaction mapping of τ phosphotyrosine sites with SH2 domains in the human genome: Implications for the rational design of self-inhibitory phosphopeptides to target τ hyperphosphorylation signaling in Alzheimer’s Disease
      TCR/CD3
        Structural basis of assembly of the human T cell receptor-CD3 complex
        The structural basis of T-cell receptor (TCR) activation: An enduring enigma
  art
    The LEGO® brick road to open science and biotechnology
  health
    wearable biosensor
      Wearable biosensors for healthcare monitoring
      Recent developments in sensors for wearable device applications
    aging
      review
        Dissecting Aging and Senescence-Current Concepts and Open Lessons
        Ageing as developmental decay: insights from p16(INK4a.)
        Human age reversal: Fact or fiction?
      NMN
        Nicotinamide mononucleotide (NMN) as an anti-aging health product - Promises and safety concerns
        Nicotinamide mononucleotide increases muscle insulin sensitivity in prediabetic women
        Benefits of Metformin in Attenuating the Hallmarks of Aging
      resveratrol
        Mechanisms of Aging and the Preventive Effects of Resveratrol on Age-Related Diseases
    diet
      Effects of Nutritional Supplements and Dietary Interventions on Cardiovascular Outcomes: An Umbrella Review and Evidence Map
      Dietary protein intake and human health
なにを（sequence, structure, function)
なにを（general, antibody)
どうやって（minimal, rational, computational, deep learning)
interface+scaffoldを含む