{"about":{"non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","site":"https://codewithpapers.app","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page","syntology":{"site":"https://syntology.ai","developers":"https://syntology.ai/developers","mcp":{"server":"https://syntology.ai/mcp","transport":"streamable-http","server_card":"https://syntology.ai/.well-known/mcp/server-card.json","auth":{"type":"trial token, no account","trial_token":"https://syntology.ai/api/oauth/trial/token","method":"POST","docs":"https://syntology.ai/developers"}},"have":"https://syntology.ai/api/graph/have?x=<method, arXiv id or title> (free, answers coverage only)","paper_base":"https://syntology.ai/paper/","atlas_base":"https://app.syntology.ai/?focus="},"machine_readable":[{"url":"https://codewithpapers.app/llms.txt","what":"the machine catalog: every machine-readable file, counted"},{"url":"https://codewithpapers.app/index/manifest.json","what":"paper-to-code index by arXiv id, with Syntology's counts"},{"url":"https://codewithpapers.app/search/manifest.json","what":"site search index (titles, authors) and its files"},{"url":"https://codewithpapers.app/download","what":"bulk files: Syntology's layer, described there"},{"url":"https://codewithpapers.app/build_manifest.json","what":"the build record: inputs, counts, exclusions, probes"}]},"url":"/task/drug-design/papers/4","list_of":"/task/drug-design","task":"Drug Design","archive":{"snapshot":"2025-07-28"},"key_notes":{"n_ran_checked":"legacy name, kept unchanged so existing readers do not break: it counts the samples that ran with no instrument failure (honoured, violated, and ran with no contract checked); it does not mean a contract was checked, and the pages print it as 'K with no instrument failure', not 'K checked'","n_constructed":"a sub-count of the samples that ran, never subtracted from them and never a failure: an executed sample whose run returned an instance of its own class (fixture_out_type equals the entry name): the run built an object and did not compute a result (Syntology's RAN record, counts.constructed)"},"syntology_read_at":"2026-09-28T10:30:06+00:00","order":"archive","order_definition":"repositories listed in the archive (most first), then date (newest first), then slug","page":4,"pages_in_order":5,"rows_per_page":100,"rows":[301,400],"of":440,"counts":{"archive_papers_tagged":440,"with_a_code_link":180,"where_syntology_ran_a_sample":66,"not_listed_spam_title":0,"listed":440,"listed_where_code_ran":66,"where_syntology_ran_a_sample_split":{"with_a_run_with_no_instrument_failure":58,"every_run_a_failure_of_syntologys_instrument":8,"listed_with_a_run_with_no_instrument_failure":58,"listed_every_run_a_failure_of_syntologys_instrument":8,"filter":{"states":["a run with no instrument failure","any run, instrument failures included"],"default":"a run with no instrument failure","note":"on the 'only where code ran' pages the default hides, in the browser, the rows where every run was a failure of Syntology's instrument; the second state shows them again. Rows are hidden, never re-ordered; these twins list every row"}},"definition":"distinct papers the archive tags; 'where Syntology ran a sample' counts papers with at least one harvested sample that ran, which is not a correctness claim"},"first_page":"/task/drug-design","prev":"/task/drug-design/papers/3","next":"/task/drug-design/papers/5","papers":[{"url":null,"slug":"shape-conditioned-3d-molecule-generation-via","title":"Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models","date":"2023-08-23","arxiv_id":"2308.11890","repositories_listed":0,"syntology":null},{"url":null,"slug":"curvature-based-transformer-for-molecular","title":"CTAGE: Curvature-Based Topology-Aware Graph Embedding for Learning Molecular Representations","date":"2023-07-25","arxiv_id":"2307.13275","repositories_listed":0,"syntology":null},{"url":null,"slug":"geometric-constraints-in-probabilistic","title":"Geometric Constraints in Probabilistic Manifolds: A Bridge from Molecular Dynamics to Structured Diffusion Processes","date":"2023-07-10","arxiv_id":"2307.04493","repositories_listed":0,"syntology":null},{"url":null,"slug":"reactie-enhancing-chemical-reaction","title":"ReactIE: Enhancing Chemical Reaction Extraction with Weak Supervision","date":"2023-07-04","arxiv_id":"2307.01448","repositories_listed":0,"syntology":null},{"url":null,"slug":"meta-path-based-probabilistic-soft-logic-for","title":"Meta-Path-based Probabilistic Soft Logic for Drug-Target Interaction Prediction","date":"2023-06-25","arxiv_id":"2306.13770","repositories_listed":0,"syntology":null},{"url":null,"slug":"synergpt-in-context-learning-for-personalized","title":"SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design","date":"2023-06-19","arxiv_id":"2307.11694","repositories_listed":0,"syntology":null},{"url":null,"slug":"happy-people-image-synthesis-as-black-box","title":"Happy People -- Image Synthesis as Black-Box Optimization Problem in the Discrete Latent Space of Deep Generative Models","date":"2023-06-11","arxiv_id":"2306.06684","repositories_listed":0,"syntology":null},{"url":null,"slug":"phen-dc-3-induces-refolding-of-human","title":"Phen-DC 3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation","date":"2023-06-07","arxiv_id":"2306.04291","repositories_listed":0,"syntology":null},{"url":null,"slug":"balancing-exploration-and-exploitation","title":"Balancing Exploration and Exploitation: Disentangled $β$-CVAE in De Novo Drug Design","date":"2023-06-02","arxiv_id":"2306.01683","repositories_listed":0,"syntology":null},{"url":null,"slug":"approximation-generalization-trade-offs-under","title":"Approximation-Generalization Trade-offs under (Approximate) Group Equivariance","date":"2023-05-27","arxiv_id":"2305.17592","repositories_listed":0,"syntology":null},{"url":null,"slug":"lingo3dmol-generation-of-a-pocket-based-3d","title":"Generation of 3D Molecules in Pockets via Language Model","date":"2023-05-17","arxiv_id":"2305.10133","repositories_listed":0,"syntology":null},{"url":null,"slug":"in-silico-approaches-to-deliver-better","title":"In Silico Approaches to Deliver Better Antibodies by Design: The Past, the Present and the Future","date":"2023-05-12","arxiv_id":"2305.07488","repositories_listed":0,"syntology":null},{"url":null,"slug":"knowledge-graph-enhanced-molecular","title":"Knowledge graph-enhanced molecular contrastive learning with functional prompt","date":"2023-05-04","arxiv_id":null,"repositories_listed":0,"syntology":null},{"url":null,"slug":"optimizing-drug-design-by-merging-generative","title":"Optimizing Drug Design by Merging Generative AI With Active Learning Frameworks","date":"2023-05-04","arxiv_id":"2305.06334","repositories_listed":0,"syntology":null},{"url":null,"slug":"evaluation-of-gpt-and-bert-based-models-on","title":"Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text","date":"2023-03-30","arxiv_id":"2303.17728","repositories_listed":0,"syntology":null},{"url":null,"slug":"molecular-property-prediction-by-semantic","title":"Molecular Property Prediction by Semantic-invariant Contrastive Learning","date":"2023-03-13","arxiv_id":"2303.06902","repositories_listed":0,"syntology":null},{"url":null,"slug":"infinite-physical-monkey-do-deep-learning","title":"Infinite Physical Monkey: Do Deep Learning Methods Really Perform Better in Conformation Generation?","date":"2023-03-08","arxiv_id":"2304.10494","repositories_listed":0,"syntology":null},{"url":null,"slug":"accurate-free-energy-estimations-of-molecular","title":"Accurate Free Energy Estimations of Molecular Systems Via Flow-based Targeted Free Energy Perturbation","date":"2023-02-23","arxiv_id":"2302.11855","repositories_listed":0,"syntology":null},{"url":null,"slug":"machine-learning-for-the-prediction-of-safe","title":"Machine learning for the prediction of safe and biologically active organophosphorus molecules","date":"2023-02-21","arxiv_id":"2302.10952","repositories_listed":0,"syntology":null},{"url":null,"slug":"do-deep-learning-models-really-outperform","title":"Do Deep Learning Models Really Outperform Traditional Approaches in Molecular Docking?","date":"2023-02-14","arxiv_id":"2302.07134","repositories_listed":0,"syntology":null},{"url":null,"slug":"prefixmol-target-and-chemistry-aware-molecule","title":"PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embedding","date":"2023-02-14","arxiv_id":"2302.07120","repositories_listed":0,"syntology":null},{"url":null,"slug":"3d-molecular-generation-via-virtual-dynamics","title":"3D Molecular Generation via Virtual Dynamics","date":"2023-02-12","arxiv_id":"2302.05847","repositories_listed":0,"syntology":null},{"url":null,"slug":"transfer-learning-for-bayesian-optimization-a","title":"Transfer Learning for Bayesian Optimization: A Survey","date":"2023-02-12","arxiv_id":"2302.05927","repositories_listed":0,"syntology":null},{"url":null,"slug":"protein-protein-docking-using-a-tensor-train","title":"Protein-protein docking using a tensor train black-box optimization method","date":"2023-02-07","arxiv_id":"2302.03410","repositories_listed":0,"syntology":null},{"url":null,"slug":"data-efficient-protein-3d-geometric","title":"Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy","date":"2023-02-05","arxiv_id":"2302.10888","repositories_listed":0,"syntology":null},{"url":null,"slug":"persistent-dirac-for-molecular-representation","title":"Persistent Dirac for molecular representation","date":"2023-02-05","arxiv_id":"2302.02386","repositories_listed":0,"syntology":null},{"url":null,"slug":"stridernet-a-graph-reinforcement-learning","title":"StriderNET: A Graph Reinforcement Learning Approach to Optimize Atomic Structures on Rough Energy Landscapes","date":"2023-01-29","arxiv_id":"2301.12477","repositories_listed":0,"syntology":null},{"url":null,"slug":"synthesis-driven-design-of-3d-molecules-for","title":"Synthesis-driven design of 3D molecules for structure-based drug discovery using geometric transformers","date":"2022-12-31","arxiv_id":"2301.00167","repositories_listed":0,"syntology":null},{"url":null,"slug":"edog-adversarial-edge-detection-for-graph","title":"EDoG: Adversarial Edge Detection For Graph Neural Networks","date":"2022-12-27","arxiv_id":"2212.13607","repositories_listed":0,"syntology":null},{"url":null,"slug":"xtrimoabfold-improving-antibody-structure","title":"xTrimoABFold: De novo Antibody Structure Prediction without MSA","date":"2022-11-30","arxiv_id":"2212.00735","repositories_listed":0,"syntology":null},{"url":null,"slug":"probabilistic-thermal-stability-prediction","title":"Probabilistic thermal stability prediction through sparsity promoting transformer representation","date":"2022-11-10","arxiv_id":"2211.05698","repositories_listed":0,"syntology":null},{"url":null,"slug":"interpreting-chemical-words-of-a-data-driven","title":"Exploring Data-Driven Chemical SMILES Tokenization Approaches to Identify Key Protein-Ligand Binding Moieties","date":"2022-10-26","arxiv_id":"2210.14642","repositories_listed":0,"syntology":null},{"url":null,"slug":"structure-based-drug-design-with-geometric","title":"Structure-based drug design with geometric deep learning","date":"2022-10-19","arxiv_id":"2210.11250","repositories_listed":0,"syntology":null},{"url":null,"slug":"immunolingo-linguistics-based-formalization","title":"ImmunoLingo: Linguistics-based formalization of the antibody language","date":"2022-09-26","arxiv_id":"2209.12635","repositories_listed":0,"syntology":null},{"url":null,"slug":"widely-used-and-fast-de-novo-drug-design-by-a","title":"Widely Used and Fast De Novo Drug Design by a Protein Sequence-Based Reinforcement Learning Model","date":"2022-08-14","arxiv_id":"2209.07405","repositories_listed":0,"syntology":null},{"url":null,"slug":"literature-review-graph-kernels-in","title":"Literature Review: Graph Kernels in Chemoinformatics","date":"2022-08-09","arxiv_id":"2208.04929","repositories_listed":0,"syntology":null},{"url":null,"slug":"a-ligand-and-structure-dual-driven-deep","title":"A Ligand-and-structure Dual-driven Deep Learning Method for the Discovery of Highly Potent GnRH1R Antagonist to treat Uterine Diseases","date":"2022-07-23","arxiv_id":"2207.11547","repositories_listed":0,"syntology":null},{"url":null,"slug":"low-cost-prediction-of-probability","title":"Low cost prediction of probability distributions of molecular properties for early virtual screening","date":"2022-07-21","arxiv_id":"2207.11174","repositories_listed":0,"syntology":null},{"url":null,"slug":"prediction-of-protein-allosteric-signalling","title":"Prediction of protein allosteric signalling pathways and functional residues through paths of optimised propensity","date":"2022-07-14","arxiv_id":"2207.07202","repositories_listed":0,"syntology":null},{"url":null,"slug":"autonomous-drug-design-with-multi-armed","title":"Autonomous Drug Design with Multi-Armed Bandits","date":"2022-07-04","arxiv_id":"2207.01393","repositories_listed":0,"syntology":null},{"url":null,"slug":"loggene-a-smooth-alternative-to-check-loss","title":"LogGENE: A smooth alternative to check loss for Deep Healthcare Inference Tasks","date":"2022-06-19","arxiv_id":"2206.09333","repositories_listed":0,"syntology":null},{"url":null,"slug":"scattersample-diversified-label-sampling-for","title":"ScatterSample: Diversified Label Sampling for Data Efficient Graph Neural Network Learning","date":"2022-06-09","arxiv_id":"2206.04255","repositories_listed":0,"syntology":null},{"url":null,"slug":"one-way-explainability-isn-t-the-message","title":"One-way Explainability Isn't The Message","date":"2022-05-05","arxiv_id":"2205.08954","repositories_listed":0,"syntology":null},{"url":null,"slug":"molecule-generation-for-drug-design-a-graph","title":"Molecule Generation for Drug Design: a Graph Learning Perspective","date":"2022-02-18","arxiv_id":"2202.09212","repositories_listed":0,"syntology":null},{"url":null,"slug":"interactivity-the-missing-link-between","title":"Interactivity: the missing link between virtual reality technology and drug discovery pipelines","date":"2022-02-08","arxiv_id":"2202.03953","repositories_listed":0,"syntology":null},{"url":null,"slug":"geneonet-a-new-machine-learning-paradigm","title":"GENEOnet: A new machine learning paradigm based on Group Equivariant Non-Expansive Operators. An application to protein pocket detection","date":"2022-01-31","arxiv_id":"2202.00451","repositories_listed":0,"syntology":null},{"url":null,"slug":"molecule-generation-from-input-attributions","title":"Molecule Generation from Input-Attributions over Graph Convolutional Networks","date":"2022-01-25","arxiv_id":"2202.05703","repositories_listed":0,"syntology":null},{"url":null,"slug":"semi-supervised-gcn-for-learning-molecular","title":"Semi-Supervised GCN for learning Molecular Structure-Activity Relationships","date":"2022-01-25","arxiv_id":"2202.05704","repositories_listed":0,"syntology":null},{"url":null,"slug":"alphafold-accelerates-artificial-intelligence","title":"AlphaFold Accelerates Artificial Intelligence Powered Drug Discovery: Efficient Discovery of a Novel Cyclin-dependent Kinase 20 (CDK20) Small Molecule Inhibitor","date":"2022-01-21","arxiv_id":"2201.09647","repositories_listed":0,"syntology":null},{"url":null,"slug":"reinforcement-learning-for-personalized-drug","title":"Reinforcement Learning for Personalized Drug Discovery and Design for Complex Diseases: A Systems Pharmacology Perspective","date":"2022-01-21","arxiv_id":"2201.08894","repositories_listed":0,"syntology":null},{"url":null,"slug":"frequent-itemset-driven-search-for-finding","title":"Frequent Itemset-driven Search for Finding Minimum Node Separators in Complex Networks","date":"2022-01-18","arxiv_id":"2201.06877","repositories_listed":0,"syntology":null},{"url":null,"slug":"a-constraint-programming-approach-to-weighted","title":"A Constraint Programming Approach to Weighted Isomorphic Mapping of Fragment-based Shape Signatures","date":"2021-12-20","arxiv_id":"2112.10892","repositories_listed":0,"syntology":null},{"url":null,"slug":"feature-importance-aware-graph-attention","title":"Learning to Detect Critical Nodes in Sparse Graphs via Feature Importance Awareness","date":"2021-12-03","arxiv_id":"2112.03404","repositories_listed":0,"syntology":null},{"url":null,"slug":"cells-cost-effective-evolution-in-latent","title":"HelixMO: Sample-Efficient Molecular Optimization in Scene-Sensitive Latent Space","date":"2021-11-30","arxiv_id":"2112.00905","repositories_listed":0,"syntology":null},{"url":null,"slug":"ai-challenges-for-predicting-the-impact-of","title":"AI challenges for predicting the impact of mutations on protein stability","date":"2021-11-08","arxiv_id":"2111.04208","repositories_listed":0,"syntology":null},{"url":null,"slug":"structure-aware-generation-of-drug-like","title":"Structure-aware generation of drug-like molecules","date":"2021-11-07","arxiv_id":"2111.04107","repositories_listed":0,"syntology":null},{"url":null,"slug":"de-novo-molecular-generation-with-stacked","title":"De Novo Molecular Generation with Stacked Adversarial Model","date":"2021-10-24","arxiv_id":"2110.12454","repositories_listed":0,"syntology":null},{"url":null,"slug":"molecular-graph-generation-via-geometric-1","title":"Molecular Graph Generation via Geometric Scattering","date":"2021-10-12","arxiv_id":"2110.06241","repositories_listed":0,"syntology":null},{"url":null,"slug":"an-in-depth-summary-of-recent-artificial","title":"An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design","date":"2021-10-10","arxiv_id":"2110.05478","repositories_listed":0,"syntology":null},{"url":null,"slug":"reinforcement-learning-with-real-time-docking","title":"Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design","date":"2021-10-05","arxiv_id":"2110.01806","repositories_listed":0,"syntology":null},{"url":"/paper/hit-and-lead-discovery-with-explorative-rl","slug":"hit-and-lead-discovery-with-explorative-rl","title":"Hit and Lead Discovery with Explorative RL and Fragment-based Molecule Generation","date":"2021-10-04","arxiv_id":"2110.01219","repositories_listed":0,"syntology":{"n":5,"n_ran":4,"n_constructed":0,"n_ran_checked":3,"n_instrument":1,"n_unverified":1,"n_honours":0,"n_violates":0,"n_no_contract":3,"n_pointer_only":2,"phrase":"4 ran (of which 0 constructed an object rather than computing a result; 3 with no instrument failure: 0 honoured, 0 violated, 3 with no contract checked; 1 where Syntology's instrument failed) · 1 unverified","sample_list":"/paper/hit-and-lead-discovery-with-explorative-rl#ran","syntology_url":"https://syntology.ai/paper/2110.01219","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2110.01219"}},"official":null}},{"url":null,"slug":"pharmacoprint-a-combination-of-pharmacophore","title":"Pharmacoprint -- a combination of pharmacophore fingerprint and artificial intelligence as a tool for computer-aided drug design","date":"2021-10-04","arxiv_id":"2110.01339","repositories_listed":0,"syntology":null},{"url":null,"slug":"knowledge-guided-geometric-editing-for","title":"Knowledge Guided Geometric Editing for Unsupervised Drug Design","date":"2021-09-29","arxiv_id":null,"repositories_listed":0,"syntology":null},{"url":null,"slug":"deep-denerative-models-for-drug-design-and","title":"Deep Denerative Models for Drug Design and Response","date":"2021-09-14","arxiv_id":"2109.06469","repositories_listed":0,"syntology":null},{"url":null,"slug":"training-a-discrete-variational-autoencoder","title":"Hybrid quantum-classical machine learning for generative chemistry and drug design","date":"2021-08-26","arxiv_id":"2108.11644","repositories_listed":0,"syntology":null},{"url":null,"slug":"apobind-a-dataset-of-ligand-unbound-protein","title":"APObind: A Dataset of Ligand Unbound Protein Conformations for Machine Learning Applications in De Novo Drug Design","date":"2021-08-23","arxiv_id":"2108.09926","repositories_listed":0,"syntology":null},{"url":null,"slug":"new-candidates-for-furin-inhibition-as","title":"New Candidates for Furin Inhibition as Probable Treat for COVID-19: Docking Output","date":"2021-07-27","arxiv_id":"2107.12799","repositories_listed":0,"syntology":null},{"url":null,"slug":"machine-learning-implicit-solvation-for","title":"Machine Learning Implicit Solvation for Molecular Dynamics","date":"2021-06-14","arxiv_id":"2106.07492","repositories_listed":0,"syntology":null},{"url":null,"slug":"weakly-supervised-graph-meta-learning-for-few","title":"Robust Graph Meta-learning for Weakly-supervised Few-shot Node Classification","date":"2021-06-12","arxiv_id":"2106.06873","repositories_listed":0,"syntology":null},{"url":null,"slug":"realistic-molecule-optimization-on-a-learned","title":"Realistic molecule optimization on a learned graph manifold","date":"2021-06-03","arxiv_id":"2106.13318","repositories_listed":0,"syntology":null},{"url":null,"slug":"retro-drug-design-from-target-properties-to","title":"Retro Drug Design: From Target Properties to Molecular Structures","date":"2021-05-11","arxiv_id":"2105.05220","repositories_listed":0,"syntology":null},{"url":null,"slug":"tfold-tr-combining-deep-learning-enhanced","title":"tFold-TR: Combining Deep Learning Enhanced Hybrid Potential Energy for Template-Based Modeling Structure Refinement","date":"2021-05-10","arxiv_id":"2105.04350","repositories_listed":0,"syntology":null},{"url":null,"slug":"combating-small-molecule-aggregation-with","title":"Combating small molecule aggregation with machine learning","date":"2021-05-01","arxiv_id":"2105.00267","repositories_listed":0,"syntology":null},{"url":null,"slug":"using-the-structural-kinome-to-systematize","title":"Using the structural kinome to systematize kinase drug discovery","date":"2021-04-27","arxiv_id":"2104.13146","repositories_listed":0,"syntology":null},{"url":null,"slug":"learning-to-design-drug-like-molecules-in","title":"Learning to design drug-like molecules in three-dimensional space using deep generative models","date":"2021-04-17","arxiv_id":"2104.08474","repositories_listed":0,"syntology":null},{"url":null,"slug":"resatom-system-protein-and-ligand-affinity","title":"ResAtom System: Protein and Ligand Affinity Prediction Model Based on Deep Learning","date":"2021-04-17","arxiv_id":"2105.05125","repositories_listed":0,"syntology":null},{"url":null,"slug":"artificial-intelligence-based-autonomous","title":"Artificial Intelligence based Autonomous Molecular Design for Medical Therapeutic: A Perspective","date":"2021-02-10","arxiv_id":"2102.06045","repositories_listed":0,"syntology":null},{"url":null,"slug":"paravs-a-simple-fast-efficient-and-flexible","title":"ParaVS: A Simple, Fast, Efficient and Flexible Graph Neural Network Framework for Structure-Based Virtual Screening","date":"2021-02-08","arxiv_id":"2102.06086","repositories_listed":0,"syntology":null},{"url":null,"slug":"learning-to-search-for-fast-maximum-common","title":"Learning to Search for Fast Maximum Common Subgraph Detection","date":"2021-01-01","arxiv_id":null,"repositories_listed":0,"syntology":null},{"url":null,"slug":"calotropin-from-milk-of-calotropis-gigantean","title":"Calotropin from milk of Calotropis gigantean a potent inhibitor of COVID 19 corona virus infection by Molecular docking studies","date":"2020-12-11","arxiv_id":"2012.06139","repositories_listed":0,"syntology":null},{"url":null,"slug":"retrognn-approximating-retrosynthesis-by","title":"RetroGNN: Approximating Retrosynthesis by Graph Neural Networks for De Novo Drug Design","date":"2020-11-25","arxiv_id":"2011.13042","repositories_listed":0,"syntology":null},{"url":null,"slug":"inverted-repeats-in-coronavirus-sars-cov-2","title":"Inverted repeats in coronavirus SARS-CoV-2 genome and implications in evolution","date":"2020-11-24","arxiv_id":"2011.12350","repositories_listed":0,"syntology":null},{"url":null,"slug":"scaffold-constrained-molecular-generation","title":"Scaffold-constrained molecular generation","date":"2020-09-15","arxiv_id":"2009.07778","repositories_listed":0,"syntology":null},{"url":null,"slug":"surveying-the-side-chain-network-approach-to","title":"Surveying the side-chain network approach to protein structure and dynamics: The SARS-CoV-2 spike protein as an illustrative case","date":"2020-09-09","arxiv_id":"2009.04438","repositories_listed":0,"syntology":null},{"url":null,"slug":"pre-training-of-graph-neural-network-for","title":"Pre-training of Graph Neural Network for Modeling Effects of Mutations on Protein-Protein Binding Affinity","date":"2020-08-28","arxiv_id":"2008.12473","repositories_listed":0,"syntology":null},{"url":null,"slug":"graph-convolution-neural-network-based","title":"Graph-convolution neural network-based flexible docking utilizing coarse-grained distance matrix","date":"2020-08-27","arxiv_id":"2008.12027","repositories_listed":0,"syntology":null},{"url":null,"slug":"research-and-development-of-molaical-for-drug","title":"Research and development of MolAICal for drug design via deep learning and classical programming","date":"2020-06-17","arxiv_id":"2006.09747","repositories_listed":0,"syntology":null},{"url":null,"slug":"interactionnet-modeling-and-explaining-of","title":"InteractionNet: Modeling and Explaining of Noncovalent Protein-Ligand Interactions with Noncovalent Graph Neural Network and Layer-Wise Relevance Propagation","date":"2020-05-12","arxiv_id":"2005.13438","repositories_listed":0,"syntology":null},{"url":null,"slug":"evolutionary-multi-objective-design-of-sars","title":"Evolutionary Multi-Objective Design of SARS-CoV-2 Protease Inhibitor Candidates","date":"2020-05-06","arxiv_id":"2005.02666","repositories_listed":0,"syntology":null},{"url":null,"slug":"computing-absolute-free-energy-with-deep","title":"Computing Absolute Free Energy with Deep Generative Models","date":"2020-05-01","arxiv_id":"2005.00638","repositories_listed":0,"syntology":null},{"url":null,"slug":"molecular-design-in-synthetically-accessible","title":"Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement Learning","date":"2020-04-29","arxiv_id":"2004.14308","repositories_listed":0,"syntology":null},{"url":null,"slug":"recognition-of-potential-covid-19-drug","title":"Recognition of potential Covid-19 drug treatments through the study of existing protein-drug and protein-protein structures: an analysis of kinetically active residues","date":"2020-04-21","arxiv_id":"2004.10233","repositories_listed":0,"syntology":null},{"url":null,"slug":"continuous-representation-of-molecules-using","title":"Continuous Representation of Molecules Using Graph Variational Autoencoder","date":"2020-04-17","arxiv_id":"2004.08152","repositories_listed":0,"syntology":null},{"url":null,"slug":"molecular-docking-studies-on-jensenone-from","title":"Molecular docking studies on Jensenone from eucalyptus essential oil as a potential inhibitor of COVID 19 corona virus infection","date":"2020-04-17","arxiv_id":"2004.00217","repositories_listed":0,"syntology":null},{"url":null,"slug":"target-specific-and-selective-drug-design-for","title":"CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models","date":"2020-04-02","arxiv_id":"2004.01215","repositories_listed":0,"syntology":null},{"url":null,"slug":"application-and-assessment-of-deep-learning","title":"Application and Assessment of Deep Learning for the Generation of Potential NMDA Receptor Antagonists","date":"2020-03-31","arxiv_id":"2003.14360","repositories_listed":0,"syntology":null},{"url":null,"slug":"direct-coupling-analysis-of-epistasis-in","title":"Direct Coupling Analysis of Epistasis in Allosteric Materials","date":"2020-03-13","arxiv_id":"1811.10480","repositories_listed":0,"syntology":null},{"url":null,"slug":"old-drugs-for-newly-emerging-viral-disease","title":"Old Drugs for Newly Emerging Viral Disease, COVID-19: Bioinformatic Prospective","date":"2020-03-10","arxiv_id":"2003.04524","repositories_listed":0,"syntology":null},{"url":null,"slug":"persistent-spectral-based-machine-learning","title":"Persistent spectral based machine learning (PerSpect ML) for drug design","date":"2020-02-03","arxiv_id":"2002.00582","repositories_listed":0,"syntology":null},{"url":null,"slug":"learning-of-signaling-networks-molecular","title":"Learning of signaling networks: molecular mechanisms","date":"2020-01-31","arxiv_id":"2001.11679","repositories_listed":0,"syntology":null}],"record_sha256":"f60605d1dc051b57c11202ba9ef62f1f19b5edda3823a12103b5067807d123d6","record_changed_at":"2026-09-28","record_changed_at_basis":"first_hashed"}