📚 月次論文レビュー総括レポート

対象期間: 2026-04-01 〜 2026-04-30生成日時: 2026-04-26
286
総論文数
286
スライドあり
30
サブページ数
3
カテゴリ数

📂 カテゴリ別サブページ

10件超のカテゴリは10件ごとに分割されています。各ページで実装/精読/後回しのトリアージが可能です。

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機械学習・AI
165 本
スライドあり: 165 本 · 17 ページ
📄 ページ1: 1〜10件📄 ページ2: 11〜20件📄 ページ3: 21〜30件📄 ページ4: 31〜40件📄 ページ5: 41〜50件📄 ページ6: 51〜60件📄 ページ7: 61〜70件📄 ページ8: 71〜80件📄 ページ9: 81〜90件📄 ページ10: 91〜100件📄 ページ11: 101〜110件📄 ページ12: 111〜120件📄 ページ13: 121〜130件📄 ページ14: 131〜140件📄 ページ15: 141〜150件📄 ページ16: 151〜160件📄 ページ17: 161〜165件
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計算化学
87 本
スライドあり: 87 本 · 9 ページ
📄 ページ1: 1〜10件📄 ページ2: 11〜20件📄 ページ3: 21〜30件📄 ページ4: 31〜40件📄 ページ5: 41〜50件📄 ページ6: 51〜60件📄 ページ7: 61〜70件📄 ページ8: 71〜80件📄 ページ9: 81〜87件
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メディシナルケミストリー
34 本
スライドあり: 34 本 · 4 ページ
📄 ページ1: 1〜10件📄 ページ2: 11〜20件📄 ページ3: 21〜30件📄 ページ4: 31〜34件

📋 論文一覧（全 286 件）

#タイトルカテゴリ発表スライド
1Porphyromonas gingivalis in Alzheimer's disease brains: Evidence for disease causation and treatment…メディシナルケミストリー2019年1月✅
2kUPS: a molecular simulation engine for the AI era計算化学2026年4月✅
3Landscape-scale navigation unlocks antibody CDR structural logic for AI-guided rescue and therapeuti…機械学習・AI2026年4月✅
4Structure-guided molecular design with contrastive 3D protein-ligand learning機械学習・AI2026年4月✅
5Robust Inference-Time Steering of Protein Diffusion Models via Embedding Optimization機械学習・AI2026年2月✅
6Regression with Large Language Models for Materials and Molecular Property Prediction機械学習・AI2024年（arXiv プレプリント）✅
7Mol-Debate: Multi-Agent Debate Improves Structural Reasoning in Molecular Design機械学習・AI2026年4月22日（arXiv プレプリント）✅
8Multimodal Graph Fusion with Statistically Guided Parsimonious Descriptor Selection for Molecular Pr…機械学習・AI2026年（Journal of Cheminformatics, 18:18）✅
9Advancing Reproducibility and Open Data in Theoretical and Computational Chemistry計算化学2026年（J. Chem. Theory Comput. / J. Chem. Inf. Model. 連名エディトリアル）✅
10Ensemble Analyzer: An Open-Source Python Framework for Automated Conformer Ensemble Refinement計算化学2026年4月✅
11A Transformer for Reaction-Aware Compound Explorations with GFlowNet in QSAR-Guided Molecular Design機械学習・AI2026年4月（J. Chem. Inf. Model.、ASAP）✅
12Combined All-Atom Simulations and Biophysical Assays Uncover Loop-Driven Stabilization in the HRAS i…計算化学2026年3月（J. Chem. Inf. Model. 2026, 66, 3276–3287）✅
13Rise of AI Technologies in Virtual Screening機械学習・AI2026年4月（J. Chem. Inf. Model., Letter）✅
14Drug Discovery and Computational Chemistry: A State-of-the-Art Review計算化学2026年4月（ChemistrySelect、Accepted 2026-04-13）✅
15Revisiting Target-Aware de novo Molecular Generation with TarPass: Between Rational Design and Texas…計算化学2026年4月（Advanced Science、Received 2026-03-12 / Accepted 2026-04-13）✅
16Identification of KKL-35 as a novel carnosine dipeptidase 2 (CNDP2) inhibitor by in silico screening計算化学2025年9月（bioRxiv プレプリント）✅
17Supporting Medicinal Chemists in Iterative Hypothesis Generation for Drug Target Identification機械学習・AI2025年12月✅
18DynaRepo: the repository of macromolecular conformational dynamics計算化学2025年10月（Nucleic Acids Research、Database issue）✅
19MolAI: A Deep Learning Framework for Data-Driven Molecular Descriptor Generation and Advanced Drug D…機械学習・AI2025年9月（J. Chem. Inf. Model. 2025, 65, 9892–9909）✅
20SHARP: Generating Synthesizable Molecules via Fragment-Based Hierarchical Action-Space Reinforcement…機械学習・AI2025年10月（J. Chem. Inf. Model. 2025, 65, 11601–11619）✅
21VeGA: A Versatile Generative Architecture for Bioactive Molecules across Multiple Therapeutic Target…機械学習・AI2025年10月（J. Chem. Inf. Model. 2025, 65, 10918–10931）✅
22Combining GCN Structural Learning with LLM Chemical Knowledge for Enhanced Virtual Screening機械学習・AI2025年10月（J. Chem. Inf. Model. 2025, 65, 11510–11520）✅
23ChemFM as a scaling law guided foundation model pre-trained on informative chemicals機械学習・AI2025年11月（Communications Chemistry, Article in Press）✅
24LLMize: A Framework for Large Language Model-Based Numerical Optimization機械学習・AI2025年12月（arXiv プレプリント）✅
25HELM-BERT: A Transformer for Medium-Sized Peptide Property Prediction機械学習・AI2025年12月（arXiv プレプリント）✅
26aiXiv: A Next-Generation Open Access Ecosystem for Scientific Discovery Generated by AI Scientists機械学習・AI2025年8月（arXiv プレプリント、v2: 2025年12月更新）✅
27AI-Driven Molecular Design: Synergizing Deep Generative Models with Evolutionary Optimization機械学習・AI2025年11月（IConTES 2025, Antalya/Türkiye）✅
28LAMMPS-ANI: Large Scale Molecular Dynamics Simulations with ANI Neural Network Potential機械学習・AI2025年（ChemRxiv プレプリント）✅
29BindFlow: a free, user-friendly pipeline for absolute binding free energy calculations using free en…計算化学2025年9月（bioRxiv preprint）✅
30Unified all-atom molecule generation with neural fields機械学習・AI2025年11月✅
31Uncertainty-Aware Multi-Objective Reinforcement Learning-Guided Diffusion Models for 3D De Novo Mole…機械学習・AI2025年10月✅
32Lost in Tokenization: Context as the Key to Unlocking Biomolecular Understanding in Scientific LLMs機械学習・AI2025年10月✅
33Physics–Preference Aligned Tool-Using Policies for Molecular Design with Gemma-3 270M機械学習・AI2025年（NeurIPS 2025 ML4PS Workshop）✅
34Joint Design of Protein Surface and Structure Using a Diffusion Bridge Model機械学習・AI2025年11月（NeurIPS 2025）✅
35Improving protein-ligand complex generation with force field guidance機械学習・AI2025年（NeurIPS 2025 Workshop SimBioChem）✅
36Trillion Ligands per Day: Performance-Portable Virtual Screening via Compound Database Optimization …計算化学2025年11月（SC '25, St Louis, MO, USA）✅
37Integrated In Silico Pipeline for Validating AI-Generated Ligands: From Docking Consensus to Molecul…計算化学2026年（IWBBIO 2025 proceedings, LNBI 16050）✅
38Protocol for an automated virtual screening pipeline including library generation and docking evalua…計算化学2025年12月✅
39PLNet: Persistent Laplacian Neural Network for Protein–Protein Binding Free Energy Prediction機械学習・AI2025年12月✅
40Modeling Protein–Small Molecule Conformational Ensembles with PLACER機械学習・AI2025年11月✅
41Resolving Data Bias Improves Generalization in Binding Affinity Prediction機械学習・AI2025年✅
42Navigating Structure-Based Drug Discovery with Emerging Innovations in Physics- and Knowledge-Based …計算化学2025年✅
43Sampling Challenges of MM/PBSA Binding Energy Calculations計算化学2025年10月✅
44MicroCycle: An Integrated and Automated Platform to Accelerate Drug Discoveryメディシナルケミストリー2024年1月25日（J. Med. Chem. 2024, 67, 2118–2128）✅
45Evaluating Ligand Docking Methods for Drugging Protein–Protein Interfaces: Insights from AlphaFold2 …計算化学2025年（J. Cheminformatics 17:144）✅
46Computation of Protein-Ligand Binding Free Energies with a Quantum Mechanics-Based Mining Minima Alg…計算化学2025年3月（Accepted: March 3, 2025）✅
47REINFORCE-ING Chemical Language Models for Drug Discovery機械学習・AI2025年11月（Accepted: November 7, 2025）✅
48SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis計算化学2025年11月（Accepted: November 19, 2025）✅
49Boosting Drug Discovery: Expanding the Applicability of Fragment Dissolved Molecular Dynamics to Acc…計算化学2025年（JCIM ASAP）✅
50RLMolLM: Reinforcement Learning-Enhanced Language Model Framework for Inverse Molecular Design機械学習・AI2025年11月✅
51SiteMatcher: A Web Server for Structure-Based Drug Design Using Protein-Ligand Interaction Patterns計算化学2025年11月✅
52Combining AlphaFold with Focused Virtual Library Design in the Development of Novel CCR2 and CCR5 An…メディシナルケミストリー2025年（JCIM ASAP）✅
53MAPCliff-WMGR: Exploring Activity Cliffs in Molecular Activity Prediction Enhanced by Weighted Molec…機械学習・AI2025年11月✅
54Ultra-large Library Screening with an Evolutionary Algorithm in Rosetta (REvoLd)計算化学2025年✅
55A Quantitative Model of Structure-Based Virtual Screening Performance計算化学2025年✅
56FEP Ω: The End of Parameter Tuning計算化学2025年✅
57Benchmarking Active Learning Virtual Screening across Vina, Glide, and SILCS-based Docking at a Tran…計算化学2025年✅
58Rethinking Ligand Efficiency: Normalization Pitfalls, Uncertainty, and State-Invariant Metricsメディシナルケミストリー2025年11月✅
59PEGASUS: Unlocking Polarity in Cell-Permeable Cyclic Peptides Using AI Models Built on Massively Par…機械学習・AINovember 2025✅
60EDWARD: E(3)-Equivariant Dual-Way Attentive Reduction for Peptide-to-Small-Molecule Design機械学習・AIDecember 2025✅
61A QM-AI Approach for the Acceleration of Accurate Assessments of Halogen-π Interactions by Training …計算化学December 2025✅
62Improved ADME Prediction by Multitask Pretraining on Predicted Data: Insights from the ASAP-Polaris-…機械学習・AI2025年（J. Chem. Inf. Model.、掲載確定）✅
63Descriptor-First Approach for ADMET Prediction in the PolarisHub Antiviral Challenge機械学習・AI2026年1月（J. Chem. Inf. Model. 2026, 66, 406–412）✅
64BioChemAIgent: An AI-driven Protein Modeling and Docking Framework for Structure-Based Drug Discover…機械学習・AI2025年12月✅
65A unified language model bridging de novo and fragment-based 3D molecule design delivers potent CBL-…機械学習・AI2025年11月✅
66BENTO: Benchmarking Classical and AI Docking on Drug Design-Relevant Data計算化学2025年12月✅
67The Influence of Ligands on AlphaFold3 Prediction of Cryptic Pockets機械学習・AI2026年1月✅
68FlashAffinity: Bridging the Accuracy-Speed Gap in Protein-Ligand Binding Affinity Prediction機械学習・AI2025年12月✅
69Explaining how mutations affect AlphaFold predictions機械学習・AI2026年1月✅
70SeedFold: Scaling Biomolecular Structure Prediction機械学習・AI2025年12月✅
71Apo2Mol: 3D Molecule Generation via Dynamic Pocket-Aware Diffusion Models機械学習・AI2025年11月✅
72SculptDrug: A Spatial Condition-Aware Bayesian Flow Model for Structure-based Drug Design機械学習・AI2025年11月✅
73ReACT-Drug: Reaction-Template Guided Reinforcement Learning for de novo Drug Design機械学習・AI2025年12月✅
74MolGuidance: Advanced Guidance Strategies for Conditional Molecular Generation with Flow Matching機械学習・AI2025年12月✅
75Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein…機械学習・AI2025年11月✅
76Diffusion Models are Molecular Dynamics Simulators機械学習・AI2025年11月✅
77MolSculpt: Sculpting 3D Molecular Geometries from Chemical Syntax機械学習・AI2025年12月✅
78RxnBench: A Multimodal Benchmark for Evaluating Large Language Models on Chemical Reaction Understan…機械学習・AI2025年12月✅
79MDAgent2: Large Language Model for Code Generation and Knowledge Q&A in Molecular Dynamics機械学習・AI2026年1月✅
80MolAct: An Agentic RL Framework for Molecular Editing and Property Optimization機械学習・AI2025年12月✅
81HalluMat: Detecting Hallucinations in LLM-Generated Materials Science Content Through Multi-Stage Ve…機械学習・AI2025年12月✅
82FRAGMENTA: End-to-end Fragmentation-based Generative Model with Agentic Tuning for Drug Lead Optimiz…機械学習・AI2025年11月✅
83AGAPI-Agents: An Open-Access Agentic AI Platform for Accelerated Materials Design on AtomGPT.Org機械学習・AI2025年12月✅
84SCP: Accelerating Discovery with a Global Web of Autonomous Scientific Agents機械学習・AI2025年12月✅
85Understanding Structural Representation in Foundation Models for Polymers機械学習・AI2025年12月✅
86Learning to Make Decisions for Autonomous Drug Design機械学習・AI2025年（Chalmers 工科大学 + ヨーテボリ大学 博士論文）✅
87Deep contrastive learning enables genome-wide virtual screening機械学習・AI2026年1月8日✅
88Computational and experimental investigation for new transition metal selenides and sulfides: The im…計算化学2016年7月✅
89Assessing the potential of deep learning for protein–ligand docking機械学習・AI2025年（受理: 2025年11月）✅
90Monovalent pseudo-natural products supercharge degradation of IDO1 by its native E3 KLHDC3メディシナルケミストリー2026年（受理: 2025年11月）✅
91Quantum-machine-assisted drug discovery機械学習・AI2026年（npj Drug Discovery, 2026, 3:1）✅
92Extrapolating Foundation Generative Models with Physics: A Case Study of Exploring Peptide Conformat…機械学習・AI2025年12月（J. Phys. Chem. Lett. 受理）✅
93Discovery of MT-7117 (Dersimelagon Phosphoric Acid): A Novel, Potent, Selective, and Nonpeptidic Ora…メディシナルケミストリー2024年12月（J. Med. Chem. 2024, 67, 21729–21748）✅
94Highlights of Medicinal Chemistry Optimization Strategies in Peptidomimetic Antimalarial Drug Discov…メディシナルケミストリー2025年12月（J. Med. Chem. 受理）✅
95A New Fragment-Based Pharmacophore Virtual Screening Workflow Identifies Potent Inhibitors of SARS-C…計算化学2025年（J. Comput. Chem. 2025; 46:e70201）✅
96ALCHEMD: Bridging Accessibility and Accuracy in Automated Relative Binding Free Energy Workflows計算化学2025年12月（J. Chem. Theory Comput. オンライン先行公開）✅
97Automated Machine Learning Pipeline: Large Language Models-Assisted Automated Data set Generation fo…機械学習・AI2025年12月（J. Chem. Theory Comput. オンライン先行公開）✅
98DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model機械学習・AI2023年10月（bioRxiv preprint）; J. Chem. Inf. Model. 2024掲載✅
99AlphaFold-RandomWalk and AlphaFold-Ensemble: Sampling Alternative Protein Conformations with Perturb…機械学習・AI2025年12月（オンライン先行公開）✅
100Meeko: Molecule Parametrization and Software Interoperability for Docking and Beyond計算化学2025年12月✅
101Improving the Reliability of Molecular String Representations for Generative Chemistry機械学習・AI2025年✅
102Contact Parallel Cascade Selection Molecular Dynamics (cPaCS-MD) for Accurate In Silico Prediction o…計算化学2026年1月（受理: 2025年12月16日）✅
103Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging T…計算化学2025年9月✅
104TorchANI 2.0: An Extensible, High-Performance Library for the Design, Training, and Use of NN-IPs機械学習・AI2025年10月✅
105ADvisor: An Open-Source Tool for Applicability Domain Definition and Optimization in Molecular Predi…機械学習・AI2025年10月✅
106Navigating Ultralarge Virtual Chemical Spaces with Product-of-Experts Chemical Language Models機械学習・AI2024年10月✅
107ProfhEX: Empowering Early Drug Discovery with Machine Learning-Based Target Profiling and Liability …機械学習・AI2025年（受理: 2025年10月15日）✅
108gSelformer-MV: Multiview, Subgraph-Augmented Group SELFIES Transformer for Molecular Property Predic…機械学習・AI2025年（受理: 2025年12月）✅
109Can AI-Predicted Complexes Teach Machine Learning to Compute Drug Binding Affinity?機械学習・AI2025年（受理: 2025年12月）✅
110Chemprop v2: An Efficient, Modular Machine Learning Package for Chemical Property Prediction機械学習・AI2025年（受理: 2025年12月）✅
111TEMPL: A Template-Based Protein–Ligand Pose Prediction Baseline計算化学2025年10月✅
112Toward Generalizable Data-Driven Pharmacokinetics with Interpretable Neural ODEs機械学習・AI2026-02 (J. Chem. Inf. Model. 2026, 66, 2640−2650)✅
113ROSHAMBO2: Accelerating Molecular Alignment for Large Chemical Libraries with GPU Optimization and A…計算化学2025-09 (J. Chem. Inf. Model. 65, 9842−9849)✅
114The growing role of open source software in molecular modeling計算化学2026（ChemRxiv preprint, CC BY 4.0）✅
115SynFrag: Synthetic Accessibility Predictor based on Fragment Assembly Generation in Drug Discovery機械学習・AI2025（ChemRxiv preprint, CC BY 4.0）✅
116Practically Significant Method Comparison Protocols for Machine Learning in Small Molecule Drug Disc…機械学習・AI2025年9月✅
117eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems計算化学2025年11月✅
118From Obstacle to Design Advantage: Activity Cliff Aware Modeling for Small-Molecule Drug Discovery機械学習・AI2025年12月（Drug Discovery Today）✅
119Computational Approaches Enhance the Design of Molecular Glue Degraders for Undruggable Proteins計算化学2025年12月（Drug Discovery Today Vol.31 No.1 Jan 2026）✅
120Deep Learning and Molecular Dynamics Reveal Promising EZH2 Inhibitors for Epigenetic Cancer Targetin…計算化学2025年11月✅
121graphpancake: A Python package for representing organic molecules as molecular graphs utilizing elec…機械学習・AI2025（ChemRxiv preprint, MIT license）✅
122A Foundation Model for Accurate Atomistic Simulations in Drug Design機械学習・AI2025年（ChemRxiv preprint）✅
123A Systematic Review of Drug-Related Interactions Utilizing Deep Learning and LLMs for Prediction and…機械学習・AI2025年12月✅
124A Foundation Model for Accurate Atomistic Simulations in Drug Design機械学習・AI2025（ChemRxiv preprint）✅
125ChemTSv3: Generalizing Molecular Design via Flexible Search Space Control機械学習・AI2025（ChemRxiv preprint）✅
126Hybrid ChemBERTa and DFT Machine Learning Framework for Predicting Enantioselectivity in Organosilan…機械学習・AI2025（ChemRxiv preprint）✅
127Modular Assembly of Allosteric MEK Inhibitor Structural Elements Unravels Potency and Feedback-Modul…メディシナルケミストリーDecember 2015✅
128Decoding of Inconsistent Biological Data: A Critical Step toward Enhanced AI Predictivity in Drug Di…機械学習・AI2025 (online ahead of print)✅
129Discovery of Potent and Efficacious Influenza PB2 InhibitorsメディシナルケミストリーDecember 2025 (online), January 2026 (issue)✅
130Active Learning FEP Using 3D-QSAR for Prioritizing Bioisosteres in Medicinal Chemistry計算化学April 2025✅
131Application of Free Energy Perturbation (FEP) Methodology for Predicting the Binding Affinity of Mac…計算化学May 2025✅
132MSFold: Multi-State Protein Structure Prediction via Parallel Tempering in Discrete Token Space機械学習・AIMarch 2026✅
133Protenix-v1: A Fully Open-Source Structure Prediction Model Surpassing AlphaFold3機械学習・AIFebruary 2026✅
134Structural Consequences of Introducing Multiple Ionizable Residues in a Protein with a Highly Charge…計算化学March 2026✅
135G-screen: Scalable Receptor-Aware Virtual Screening through Flexible Ligand Alignment計算化学March 2026✅
136Integrating BioEmu Ensemble Sampling with Molecular Dynamics and Markov State Models for Protein Con…計算化学January 2026✅
137Beyond Bioisosteres: sp3-Rich Bicyclic Scaffolds for Improved ADME Properties in Lead Optimizationメディシナルケミストリー2026✅
138Beyond SMILES: Evaluating Agentic AI Systems for Chemistry機械学習・AIFebruary 2026✅
139DESRO: Scientific Reasoning from Outcomes via Large Language Models機械学習・AI2026✅
140SpaceGFN: Programmable Chemical Space Exploration via GFlowNet機械学習・AI2026✅
141Evaluating Boltz-2 for Protein-Ligand Binding Prediction: A Large-Scale Computational Study計算化学March 2026✅
142SciDesignBench: A Benchmark for Scientific Design Reasoning with Reinforcement Learning from Scienti…機械学習・AIMarch 2026✅
143Beyond Affinity: A Comprehensive Benchmark for Structure-Based Drug Design Methods機械学習・AIJanuary 2026✅
144TerraBind: Coarse-Grained Molecular Representations for Efficient Protein-Ligand Binding Affinity Pr…機械学習・AIFebruary 2026✅
145DrugR: Optimizing Molecular Drugs through LLM-Based Explicit Reasoning機械学習・AI2026年2月（プレプリント）✅
146Reinforcement Learning with LLM-Guided Action Spaces for Synthesizable Lead Optimization機械学習・AI2026年4月（プレプリント）✅
147Reference-Guided Policy Optimization for Molecular Optimization via LLM Reasoning機械学習・AI2026年（ICLR 2026 採択）✅
148MolEvolve: LLM-Guided Evolutionary Search for Interpretable Molecular Optimization機械学習・AI2026年3月（プレプリント）✅
149MolecularIQ: Characterizing Chemical Reasoning Capabilities Through Symbolic Verification on Molecul…機械学習・AI2026年1月（プレプリント）✅
150Ontology-to-Tools Compilation for Executable Semantic Constraint Enforcement in LLM Agents機械学習・AI2026年2月（Cambridge Centre for Computational Chemical Engineering プレプリント）✅
151Accurate Predictions of Novel Biomolecular Interactions with IsoDDE機械学習・AI2026年2月（Isomorphic Labs テクニカルレポート）✅
152Epsilon: An Autonomous Research Engine with Epistemic Integrity for Scientific Discovery機械学習・AI2026年2月（独立プレプリント）✅
153A Unified Language Model Bridging De Novo and Fragment-Based 3D Molecule Design機械学習・AI2026年2月（Research Square プレプリント）✅
154Breaking the Barriers of Molecular Dynamics With Deep-Learning: Opportunities, Pitfalls, and How to …機械学習・AI2026年（WIREs Computational Molecular Science）✅
155Fast Sampling of Protein Conformational Dynamics計算化学2026年（Science Advances）✅
156Physics Beats Diffusion: Agentic AI-Driven Virtual Screening Benchmark on a GPCR Target計算化学2026年3月（Research Square プレプリント）✅
157PROTAC Approaches against Drug-Resistant EGFR C797S/L858R/T790M Mutants: Biological Evaluation and S…メディシナルケミストリー2026年（RSC Medicinal Chemistry）✅
158DeepDegradome: A Structure-Aware Deep Learning Framework for PROTAC and Ligand Generation Against Pr…機械学習・AI2026年（PNAS）✅
159An LLM Chatbot to Facilitate Primary-to-Specialist Care Transitions: A Randomized Controlled Trial機械学習・AI2026年（Nature Medicine）✅
160Molecular Representation Matters: Comparative Evaluation of Fingerprints, RDKit Descriptors, and Has…機械学習・AI2026年（J. Phys. Chem. Lett.）✅
161In-Pocket 3D Graphs Enhance Ligand-Target Generative Small-Molecule Creation: A Dopamine D2 Receptor…機械学習・AI2026年（J. Phys. Chem. B）✅
162Large Library Docking for Polypharmacology: Simultaneous Discovery of Ligands for Multiple GPCR Targ…計算化学2026年（J. Med. Chem.）✅
163What Happens in Successful Optimizations? A Survey of 2018–2024 Literatureメディシナルケミストリー2026年（J. Med. Chem.）✅
164Tokenization for Molecular Foundation Models: A Comprehensive Evaluation機械学習・AI2026年（J. Chem. Inf. Model.）✅
165ArtiDock: Accurate Machine Learning Approach to Protein-Ligand Docking for High-Throughput Virtual S…計算化学2026年（Journal of Chemical Information and Modeling）✅
166A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules (CBFE)計算化学2026年（Journal of Chemical Information and Modeling, 66, 1626-1636）✅
167QUICK and Robust ESP and RESP Charges for Computational Biochemistry計算化学2026年（Journal of Chemical Information and Modeling, 66, 3173-3187）✅
168CHARMM-GUI Hybrid ML/MM Builder for Hybrid Machine Learning and Molecular Mechanical Simulations計算化学2026年（Journal of Chemical Information and Modeling, 66, 2960-2966）✅
169CHARMM-GUI Ligand Docker for Molecular Docking with Various Docking Programs計算化学2026年（Journal of Chemical Information and Modeling）✅
170GlueFinder: A Data-Driven Framework for the Rational Discovery of Molecular Glues計算化学2026年（Journal of Chemical Information and Modeling）✅
171DIVINE: Deterministic Top-Down Clustering Framework for Molecular Dynamics Trajectories計算化学2026年（Journal of Chemical Information and Modeling）✅
172Improving Fidelity and Diversity in Chemical Language Transformers for Inverse Molecular Design機械学習・AI2026年（Journal of Chemical Information and Modeling, 66, 3059-3073）✅
173UCBbind: More Accurate Binding Affinity Prediction via Protein Homology and Ligand-Based Transfer Le…機械学習・AI2026年（Journal of Chemical Information and Modeling, 66, 2006-2016）✅
174BOLD-GPCRs: A Transformer-Powered App for Predicting Ligand Bioactivity across Class A GPCRs機械学習・AI2026年（Journal of Chemical Information and Modeling, 66, 855-866）✅
175MolOrgGPT: De Novo Generation via Large Language Models and Reinforcement Learning機械学習・AI2026年（Journal of Chemical Information and Modeling）✅
176Large Language Model Agent for Modular Task Execution in Drug Discovery機械学習・AI2026年（Journal of Chemical Information and Modeling）✅
177UniDock-Pro: Unified GPU-Accelerated Platform for High-Throughput Virtual Screening計算化学2026年（Journal of Chemical Information and Modeling, 66, 2735-2752）✅
178A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data計算化学2026年（Journal of Chemical Information and Modeling, 66, 3129-3149）✅
179Symmetry-Sensitive Analysis of Molecular Graph Neural Network Models機械学習・AI2026年（Journal of Chemical Information and Modeling, 66, 2610-2615）✅
180CoDrug: A Text-Driven Molecular Virtual Screening and Multiproperty Optimization Framework機械学習・AI2026年（Journal of Chemical Information and Modeling）✅
181Topology-Aware Generation and Activity-Based Filtering for Data-Scarce QAC Discovery機械学習・AI2026年（Journal of Chemical Information and Modeling）✅
182Assessing Boltz-2 Performance for the Binding Classification of Docking Hits機械学習・AI2026年（Journal of Chemical Information and Modeling, 66, 1511-1521）✅
183DualBind: Dual-Module Protein-Ligand Binding Affinity Prediction with Adaptive GNN and Structure-Awa…機械学習・AI2026年（Expert Systems With Applications, Vol. 309）✅
184Discovery of Covalent Ligands with AlphaFold3計算化学2026年（JACS）✅
185Advances in Computational Methods for PROTAC Drug Discovery機械学習・AIMarch 2026 (Drug Discovery Today, Vol. 31, No. 2)✅
186Reward Function Design for Reinforcement Learning-Based Molecular Generation: Additive vs. Multiplic…機械学習・AI2025年（ChemRxiv プレプリント、Galvin/Elix）✅
187Independent Benchmarking of Boltzmann-Based Structure Prediction (Boltz-2) on ChEMBL-Derived Protein…機械学習・AI2026年（Chem-Bio Informatics Journal, Vol. 26）✅
188Hit Identification in Ultra Large Virtual Screening: An Integrative Review and Future Challenges機械学習・AI2026年1月（Drug Discovery Today）✅
189Machine Learning, Docking, or Physics for Structure Prediction of Ligand-induced Ternary Complexes機械学習・AI2026年1月（Current Opinion in Structural Biology 97:103217）✅
190NextTopDocker: The Largest-to-Date Docking Power Benchmark Reveals That Deep Learning Performs Gener…計算化学2026年2月（ChemRxiv プレプリント）✅
191Generative Virtual Screening: From Search to Generate and Back機械学習・AI2026年2月（ChemRxiv プレプリント）✅
192ChemSpace Copilot: Agentic AI for Interactive Visualization and Exploration of Chemical Space機械学習・AI2026年3月（ChemRxiv プレプリント）✅
193Transparent Acceleration of Large Library Docking with ChemSTEP計算化学2026年3月（ChemRxiv プレプリント）✅
194FragBERTa: Exploring Fragment-based Molecular Representation Learning with SAFE機械学習・AI2026年2月（ChemRxiv プレプリント）✅
195A Comparative Study of SMILES, SELFIES, and ECFP4 Representations for Molecular Similarity Search機械学習・AI2026年2月（ChemRxiv プレプリント）✅
196PyMolGen: Database-Driven Molecular Generation of Drug-Like Compounds機械学習・AI2026年3月（ChemRxiv プレプリント）✅
197A Reinforcement Learning-guided Genetic Algorithm Integrating Medicinal Chemistry-inspired Molecular…機械学習・AI2026年2月（ChemRxiv プレプリント）✅
198Docking of Millions: Accelerating a Million-Scale Virtual Screening Using Deep Learning機械学習・AI2026年3月（Briefings in Bioinformatics 27, bbag128）✅
199BBB-Permeable PROTACs: Where Do We Stand?メディシナルケミストリー2026年（ACS Medicinal Chemistry Letters）✅
200Machine Learning for De Novo Molecular Generation: A Comprehensive Review機械学習・AI2026年（ACS Chemical Neuroscience 17, 666-680）✅
201From Prompt to Drug: Toward Pharmaceutical Superintelligence機械学習・AI2026年（ACS Central Science）✅
202PROTACs in Targeted Protein Degradation: Advances in Development and AI-Enhanced Drug Discovery機械学習・AI2026年3月（European Journal of Medicinal Chemistry Reports）✅
203AI-aided Drug Development for Protein Degraders: Design, Lead Identification, and Optimization機械学習・AI2025年（Annual Reports in Medicinal Chemistry 65）✅
204The Statistical Software Revolution in Pharmaceutical Development: Challenges and Opportunities in O…機械学習・AI2026年1月（Drug Discovery Today）✅
205New Approach Methodologies for Drug Discovery機械学習・AI2026年4月（Cell 189）✅
206Steering Semi-Flexible Molecular Diffusion Model for Structure-Based Drug Design with Reinforcement …機械学習・AI2026年4月（Science Advances 12, eady9955）✅
207Construction of a Multi-label Odor Prediction Model Based on Molecular Structures and Olfactory Rece…機械学習・AI2026年（Analytical Sciences）✅
208KIMMDY: A Biomolecular Reaction Emulator計算化学2026年（Nature Communications 17:3500）✅
209Structural Optimization of Drug Molecules with Incrementally Trained Language Models機械学習・AI2026年（Nature Communications 17:3456）✅
210Harnessing AI to Build Virtual Cells機械学習・AI2026年4月（bioRxiv）✅
211UBio-MolFM: A Universal Molecular Foundation Model for Bio-Systems機械学習・AI2026年4月（preprint）✅
212MolMem: Memory-Augmented Agentic Reinforcement Learning for Sample-Efficient Molecular Optimization機械学習・AI2026年4月（preprint）✅
213MarS-FM: Generative Modeling of Molecular Dynamics via Markov State Models機械学習・AI2026年（preprint）✅
214Tabular Foundation Models for In-Context Prediction of Molecular Properties機械学習・AI2026年4月（preprint）✅
215How Creative Are Large Language Models in Generating Molecules?機械学習・AI2026年4月（preprint）✅
216Target Identification and Assessment in the Era of AI機械学習・AI2026年（Nat. Rev. Drug Discov. 2026）✅
217Chemical Space Navigation of Nitidine Leads to the Discovery of a Novel PD-L1 Degradation Agent by T…メディシナルケミストリー2026年（J. Med. Chem. 2026, 69, 8237-8254）✅
218Scaffold-Hopping Strategy on a Series of Proteasome Inhibitors Led to a Preclinical Candidate for th…メディシナルケミストリー2021年（J. Med. Chem. 2021, 64, 5905-5930）✅
219Automated Molecular Design in BRADSHAW, Applied to the Optimization of ERAP1 Inhibitorsメディシナルケミストリー2026年（J. Med. Chem. 2026, 69, 8869-8896）✅
220Discovery of YYSW001: A Highly Selective, Orally Bioavailable JAK1 Inhibitor Achieving Efficacy unde…メディシナルケミストリー2026年（J. Med. Chem. 2026, 69, 7869-7903）✅
221How to Use Quantum Computers for Biomolecular Free Energies計算化学2026年（J. Chem. Theory Comput. 2026, in press）✅
222Multiscale Hypergraph Masked Autoencoder with Δ-Property Alignment for Novel Molecular Representatio…機械学習・AI2026年（J. Chem. Inf. Model. 2026, 66, 3858-3877）✅
223ProtCross: Bridging the PDB-AlphaFold Gap for Binding Site Prediction with Protein Point Clouds機械学習・AI2026年（J. Chem. Inf. Model. 2026, 66, 3688-3701）✅
224DeepMIF: A Multiview Interactive Fusion-Based Deep Learning Method for RNA-Small Molecule Binding Af…機械学習・AI2026年（J. Chem. Inf. Model. 2026, 66, 3575-3589）✅
225Chat-Driven Computational (Bio)chemistry: Using LLM Agents to Accelerate Bio- and Chemoinformatics機械学習・AI2026年（J. Chem. Inf. Model. 2026, 66, 3397-3401）✅
226StereoMolGraph: Stereochemistry-Aware Molecular and Reaction Graphs計算化学2026年（J. Chem. Inf. Model. 2026, 66, 3830-3839）✅
227LigandExplorer: An Automated Tool for Ligand Extraction from PDB Structures計算化学2026年（J. Chem. Inf. Model. 2026, 66, 3026-3035）✅
228Unveiling the Activation Mechanism of Glucagon-Like Peptide-1 Receptor by an Ago-Allosteric Modulato…計算化学2026年（J. Chem. Inf. Model.）✅
229Efficient Binding Affinity Estimation for Fragment-Based Compounds Using a Separated Topologies Appr…計算化学2026年（J. Chem. Inf. Model.）✅
230Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization計算化学2026年（J. Chem. Inf. Model. 2026, 66, 3206-3219）✅
231AI-MedCraft: A Strategy-Driven AI Platform for Multi-Objective Molecular Design機械学習・AI2026年（J. Chem. Inf. Model. 2026, 66, 3424-3431）✅
232Doing More with Less: Accurate and Scalable Ligand Free Energy Calculations by Focusing on the Bindi…計算化学2026年（J. Chem. Inf. Model.）✅
233Improving Stereochemical Limitations in Protein-Ligand Complex Structure Prediction計算化学2025年（ACS Omega 2025, 10, 56075-56084）✅
234Evaluating the Progression of Large Language Model Capabilities for Small-Molecule Drug Design機械学習・AI2026年4月（preprint）✅
235Polyformer: a generative framework for thermodynamic modeling of polymeric molecules機械学習・AI2026年4月（preprint）✅
236The HTC-Claw: Automating Discovery through High-Throughput Computational Campaigns機械学習・AI2025年4月（preprint）✅
237UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules機械学習・AI2025年（ICML 2025）✅
238LinkLlama: Enabling Large Language Model for Chemically Reasonable Linker Design機械学習・AI2026年4月（bioRxiv preprint）✅
239AlphaFast: High-throughput AlphaFold 3 via GPU-accelerated MSA construction計算化学2026年2月（bioRxiv preprint）✅
240How to write an impactful review article?メディシナルケミストリー2026年5月（Drug Discovery Today Vol.31 No.3）✅
241Large language models for molecular design: bridging the gap between chemical syntax and biological …機械学習・AI2026年3月（Drug Discovery Today Vol.31 No.2）✅
242Toward generalizable predictive models for DNA-encoded libraries機械学習・AI2026年3月（Drug Discovery Today Vol.31 No.2）✅
243Closing the loop: Experimentally validated methods in artificial intelligence–driven protein design機械学習・AI2026年（Current Opinion in Structural Biology Vol.98）✅
244A Scaffold-Hopping Strategy on a Series of Proteasome Inhibitors Which Led to a Preclinical Candidat…メディシナルケミストリー2021年頃（J. Med. Chem. 掲載、著者 Thomas/Gilbert ら）✅
245Quantification of Hydrogen Bond Donating Ability of Biologically Relevant CompoundsメディシナルケミストリーApril 2024✅
246The Role of Allylic Strain for Conformational Control in Medicinal Chemistryメディシナルケミストリー2023✅
247Discovery and Characterization of the Potent and Selective P2X4 Inhibitor BAY-1797メディシナルケミストリーDecember 2019✅
248Eyes on Topical Ocular Disposition: Design of a Lead JAK Inhibitor with Azetidin-3-Amino Bridging Sc…メディシナルケミストリーJune 2023✅
2492025 In Review: Trends in Pharmaceutical InnovationメディシナルケミストリーMarch 2026✅
250Design, Quality and Validation of the EU-OPENSCREEN Fragment Library Poised to a High-Throughput Scr…メディシナルケミストリーApril 2024✅
251Discovery of Novel and Potent Prolyl Hydroxylase Domain-Containing Protein (PHD) Inhibitors for the …メディシナルケミストリーJanuary 2024✅
252Discovery of Tetrahydropyrazolopyrazine Derivatives as Potent and Selective MYT1 Inhibitors for the …メディシナルケミストリーJanuary 2024✅
253Escaping from Flatland: Multiparameter Optimization Leads to the Discovery of Novel Tetrahydropyrido…メディシナルケミストリーMay 2023✅
254Geminal Diheteroatomic Motifs: Some Applications of Acetals, Ketals, and Their Sulfur and Nitrogen H…メディシナルケミストリー2021✅
255Synthetic Opportunities and Challenges for Macrocyclic Kinase InhibitorsメディシナルケミストリーMay 2021✅
256Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Ta…メディシナルケミストリーNovember 2023✅
257Structure-Based Design and Evaluation of Reversible KRAS G13D InhibitorsメディシナルケミストリーDecember 2023✅
258Rapid Traversal of Ultralarge Chemical Space using Machine Learning Guided Docking Screens計算化学2023年（プレプリント）/ J. Chem. Inf. Model. 2024✅
259FragGrow: A Web Server for Structure-Based Drug Design by Fragment Growing within Constraints計算化学2024年✅
260AlphaFold2-RAVE: From Sequence to Boltzmann Ranking計算化学2023年✅
261Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2計算化学2024年✅
262Comparative Assessment of Free Energy Computational Methods for Revealing the Interactions Driving P…計算化学2026年4月（受付 2026年1月）✅
263MAIP: An Open-Source Tool to Enrich High-Throughput Screening Output and Identify Novel, Druglike Mo…機械学習・AI2023年✅
264Accelerated Chemical Reaction Optimization Using Multi-Task Learning機械学習・AI2023年✅
265Systematic Evaluation of Local and Global Machine Learning Models for the Prediction of ADME Propert…機械学習・AI2023年✅
266Molecular Deep Learning at the Edge of Chemical Space機械学習・AI2026年3月（オンライン先行公開）✅
267A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics計算化学2025年12月（Nature Communications in Press）✅
268NNP/MM: Fast Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics計算化学2022年1月（arXiv: 2201.08110），2023年（J. Chem. Inf. Model. 掲載）✅
269Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics計算化学2026年2月✅
270Artificial Intelligence for Direct Prediction of Molecular Dynamics Across Chemical Space計算化学2025年5月（arXiv），2025年〜2026年（JCTC 掲載）✅
271Ultra-Large Virtual Screening Identifies PARP-1 and FSP1 Inhibitors via Adaptive Targeting計算化学2023年4月（bioRxiv）✅
272ATMOS: Autoregressive Trajectory Model for Open-ended Simulation機械学習・AI2026年3月（arXiv）✅
273Exploring the Capabilities of Machine-Learned Potentials for Biomolecular Simulations計算化学2022年1月（arXiv）✅
274Accelerating Protein Molecular Dynamics Simulation with DeepJump計算化学2025年9月16日（arXiv）✅
275Artificial Intelligence for Direct Prediction of Molecular Dynamics Across Chemical Space計算化学2026年（arXiv）✅
276BioMD: All-atom Generative Model for Biomolecular Dynamics Simulation機械学習・AI2025年9月2日（arXiv）✅
277Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics機械学習・AI2026年2月11日（arXiv）✅
278Guidelines for the analysis of free energy calculations計算化学2015年5月（J. Comput. Aided Mol. Des. 29(5): 397–411）✅
279BIOPTIC B1 Ultra-High-Throughput Virtual Screening System Discovers LRRK2 Ligands in Vast Chemical S…機械学習・AI2025年（J. Chem. Inf. Model., accepted 2025）✅
280A bottom-up approach to find lead compounds in expansive chemical spaces計算化学2025年（Communications Chemistry）✅
281Synthon-Based Strategies Exploiting Molecular Similarity and Protein-Ligand Interactions for Efficie…計算化学2025年（J. Chem. Inf. Model., accepted April 2025）✅
282ANI Neural Networks Meet Electrostatics: A ML/MM Implementation in Amber計算化学2024年✅
283Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: …メディシナルケミストリー2023年8月✅
284When Macrocyclic Peptides Meet the Crystal Structure of a Melanocortin Receptorメディシナルケミストリー2021年（受理 2020年12月）✅
285Autonomous Diffractometry Enabled by Visual Reinforcement Learning計算化学2026年4月✅
286Consensus docking aid to model the activity of an inhibitor of DNA methyltransferase 1 inspired by d…計算化学2023年12月✅
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