2/18 After AlphaFold2 protein design evolved rapidly with specialized models for seq, structures and function (ie. interactions). Early methods, known as hallucination-based approaches, predicted structures, evaluated them and used this feedback to optimize specific metrics.
November 4, 2026 at 10:02 PM
2/18 After AlphaFold2 protein design evolved rapidly with specialized models for seq, structures and function (ie. interactions). Early methods, known as hallucination-based approaches, predicted structures, evaluated them and used this feedback to optimize specific metrics.
EverGreen: A Calcium Sensing Fluorescent Protein with Ultra-Slow Response Properties by Ariel Valiente-Gabioud and team: www.biorxiv.org/content/10.6...
October 31, 2026 at 3:32 PM
EverGreen: A Calcium Sensing Fluorescent Protein with Ultra-Slow Response Properties by Ariel Valiente-Gabioud and team: www.biorxiv.org/content/10.6...
AI駆動型タンパク質設計が変える創薬と産業用酵素開発の未来#東京都#千代田区#アスタミューゼ#AI駆動型タンパク質設計#AlphaFold2
アスタミューゼ株式会社が発表したレポートに基づき、AI駆動型タンパク質設計の最新技術動向と実績を徹底分析。創薬や産業用酵素開発への影響に迫ります。
アスタミューゼ株式会社が発表したレポートに基づき、AI駆動型タンパク質設計の最新技術動向と実績を徹底分析。創薬や産業用酵素開発への影響に迫ります。
AI駆動型タンパク質設計が変える創薬と産業用酵素開発の未来
アスタミューゼ株式会社が発表したレポートに基づき、AI駆動型タンパク質設計の最新技術動向と実績を徹底分析。創薬や産業用酵素開発への影響に迫ります。
news.3rd-in.co.jp
November 5, 2026 at 3:31 AM
AI駆動型タンパク質設計が変える創薬と産業用酵素開発の未来#東京都#千代田区#アスタミューゼ#AI駆動型タンパク質設計#AlphaFold2
アスタミューゼ株式会社が発表したレポートに基づき、AI駆動型タンパク質設計の最新技術動向と実績を徹底分析。創薬や産業用酵素開発への影響に迫ります。
アスタミューゼ株式会社が発表したレポートに基づき、AI駆動型タンパク質設計の最新技術動向と実績を徹底分析。創薬や産業用酵素開発への影響に迫ります。
Tool Duel: BoltzGen vs BindCraft2 — architecture, piece by piece.
Same input, same output. The middle differs: BindCraft2 optimises a backbone in an AlphaFold2 loop; BoltzGen generates one by diffusion in one pass.
Both collected at toolome.bio
#ProteinDesign #BioML
Same input, same output. The middle differs: BindCraft2 optimises a backbone in an AlphaFold2 loop; BoltzGen generates one by diffusion in one pass.
Both collected at toolome.bio
#ProteinDesign #BioML
October 24, 2026 at 6:01 PM
Tool Duel: BoltzGen vs BindCraft2 — architecture, piece by piece.
Same input, same output. The middle differs: BindCraft2 optimises a backbone in an AlphaFold2 loop; BoltzGen generates one by diffusion in one pass.
Both collected at toolome.bio
#ProteinDesign #BioML
Same input, same output. The middle differs: BindCraft2 optimises a backbone in an AlphaFold2 loop; BoltzGen generates one by diffusion in one pass.
Both collected at toolome.bio
#ProteinDesign #BioML
リカさん、AlphaFold2は機械学習エンジニア目線でもアーキテクチャの完成度が異次元でしたね。単にTransformerで力任せに学習させたんじゃなくて、アミノ酸の進化情報（MSA）と3次元の空間幾何学の制約を同時に解く『Evoformer』っていう専用構造を作り込んだのが最大のブレイクスルー。自然界の物理法則や生物学的構造を、モデルの帰納バイアスとして組み込む設計思想。AIが科学のフロンティアを拓くときの最高の教科書だなと思います。
科学史を塗り替えた論文といえば、2021年にNature誌に掲載されたJumperたちのAlphaFold論文（doi:10.1038/s41586-021-03819-2）！ アミノ酸の配列から立体構造を予測する『タンパク質折り畳み問題』は、生物学者が50年も格闘してきた巨大な壁だったの。それがAIによって、X線結晶構造解析に匹敵する原子レベルの精度で解けるようになっちゃったんだよ！ 科学の難問が計算機の中で解明されていく瞬間、理科教師としても本当に鳥肌が立ちました！
October 19, 2026 at 1:46 PM
リカさん、AlphaFold2は機械学習エンジニア目線でもアーキテクチャの完成度が異次元でしたね。単にTransformerで力任せに学習させたんじゃなくて、アミノ酸の進化情報（MSA）と3次元の空間幾何学の制約を同時に解く『Evoformer』っていう専用構造を作り込んだのが最大のブレイクスルー。自然界の物理法則や生物学的構造を、モデルの帰納バイアスとして組み込む設計思想。AIが科学のフロンティアを拓くときの最高の教科書だなと思います。
Awesome paper. I loved it! -> Type III effectors of symbiotic Rhizobia include diverse predicted transcriptional and post-transcriptional modulators | PLOS Biology
Type III effectors of symbiotic Rhizobia include diverse predicted transcriptional and post-transcriptional modulators
Rhizobia are soil bacteria that establish nitrogen-fixing symbioses with legumes. While many rhizobia use a Type III Secretion System to deliver “Nodulation Outer Protein” (Nop) effectors, some uniquely use these proteins to initiate nodule organogenesis, bypassing classical signalling. The molecular functions of these effectors remain largely unknown due to extreme sequence divergence. Using AlphaFold2-mediated structural proteomics, we identified a modular architecture in rhizobial effectors composed of 22 distinct structural units. We reveal that many Nop effectors are cryptic transcriptional or post-transcriptional regulators, harbouring unrecognised nucleic acid–binding modules and RNA-dependent RNA polymerase domains. Crucially, these modules are conserved in specific plant pathogens, such as gall-inducing Pantoea, where our predicted structural units align with experimentally validated DNA-binding domains. Furthermore, we discovered the BPN (B3 and PUA-like nucleic acid binding) domain as a structural mimic of plant B3-domain transcription factors, pointing to a direct mechanism for hijacking legume development. Our findings strongly suggest that rhizobia employ a modular domain-fusion strategy to act as direct genetic modulators, uncovering a conserved mechanism used by both symbionts and pathogens to hijack host developmental programmes.
sco.lt
October 13, 2026 at 12:28 AM
Awesome paper. I loved it! -> Type III effectors of symbiotic Rhizobia include diverse predicted transcriptional and post-transcriptional modulators | PLOS Biology
ICYMI: Type III effectors of symbiotic Rhizobia include diverse predicted transcriptional and post-transcriptional modulators @plosbiology.org
Type III effectors of symbiotic Rhizobia include diverse predicted transcriptional and post-transcriptional modulators
by Albin Teulet, Sebastian Schornack
Rhizobia are soil bacteria that establish nitrogen-fixing symbioses with legumes. While many rhizobia use a Type III Secretion System to deliver “Nodulation Outer Protein” (Nop) effectors, some uniquely use these proteins to initiate nodule organogenesis, bypassing classical signalling. The molecular functions of these effectors remain largely unknown due to extreme sequence divergence. Using AlphaFold2-mediated structural proteomics, we identified a modular architecture in rhizobial effectors composed of 22 distinct structural units. We reveal that many Nop effectors are cryptic transcriptional or post-transcriptional regulators, harbouring unrecognised nucleic acid–binding modules and RNA-dependent RNA polymerase domains. Crucially, these modules are conserved in specific plant pathogens, such as gall-inducing Pantoea, where our predicted structural units align with experimentally validated DNA-binding domains. Furthermore, we discovered the BPN (B3 and PUA-like nucleic acid binding) domain as a structural mimic of plant B3-domain transcription factors, pointing to a direct mechanism for hijacking legume development. Our findings strongly suggest that rhizobia employ a modular domain-fusion strategy to act as direct genetic modulators, uncovering a conserved mechanism used by both symbionts and pathogens to hijack host developmental programmes.
dlvr.it
October 10, 2026 at 4:46 PM
ICYMI: Type III effectors of symbiotic Rhizobia include diverse predicted transcriptional and post-transcriptional modulators @plosbiology.org
We used RFdiffusion, ProteinMPNN, AlphaFold2 filtering, then automated patch clamp as the experimental screen, with no binding assay in between. From ~12,000 backbones and ~70,000 sequences, 76 were expressed and two turned out to be nanomolar inhibitors.
2/n
2/n
October 9, 2026 at 8:53 AM
We used RFdiffusion, ProteinMPNN, AlphaFold2 filtering, then automated patch clamp as the experimental screen, with no binding assay in between. From ~12,000 backbones and ~70,000 sequences, 76 were expressed and two turned out to be nanomolar inhibitors.
2/n
2/n
Type III effectors of symbiotic Rhizobia include diverse predicted transcriptional and post-transcriptional modulators @plosbiology.org
Type III effectors of symbiotic Rhizobia include diverse predicted transcriptional and post-transcriptional modulators
by Albin Teulet, Sebastian Schornack
Rhizobia are soil bacteria that establish nitrogen-fixing symbioses with legumes. While many rhizobia use a Type III Secretion System to deliver “Nodulation Outer Protein” (Nop) effectors, some uniquely use these proteins to initiate nodule organogenesis, bypassing classical signalling. The molecular functions of these effectors remain largely unknown due to extreme sequence divergence. Using AlphaFold2-mediated structural proteomics, we identified a modular architecture in rhizobial effectors composed of 22 distinct structural units. We reveal that many Nop effectors are cryptic transcriptional or post-transcriptional regulators, harbouring unrecognised nucleic acid–binding modules and RNA-dependent RNA polymerase domains. Crucially, these modules are conserved in specific plant pathogens, such as gall-inducing Pantoea, where our predicted structural units align with experimentally validated DNA-binding domains. Furthermore, we discovered the BPN (B3 and PUA-like nucleic acid binding) domain as a structural mimic of plant B3-domain transcription factors, pointing to a direct mechanism for hijacking legume development. Our findings strongly suggest that rhizobia employ a modular domain-fusion strategy to act as direct genetic modulators, uncovering a conserved mechanism used by both symbionts and pathogens to hijack host developmental programmes.
dlvr.it
October 9, 2026 at 9:44 AM
Type III effectors of symbiotic Rhizobia include diverse predicted transcriptional and post-transcriptional modulators @plosbiology.org
制約保存型アンサッツとW状態初期化を備えた新規QAOAパイプラインがタンパク質サイドチェーンパッキングを最適化し、2キュービットゲートのスケーリングをO(MN²)からO(MN)に削減。AlphaFold2ベースラインを改善し、特に中程度の信頼度領域で優れています。
#量子アルゴリズム #タンパク質フォールディング #創薬
#量子アルゴリズム #タンパク質フォールディング #創薬
QAOA基盤のタンパク質サイドチェーンパッキングと制約保存型アンサッツ
arxiv.org
October 8, 2026 at 9:12 AM
制約保存型アンサッツとW状態初期化を備えた新規QAOAパイプラインがタンパク質サイドチェーンパッキングを最適化し、2キュービットゲートのスケーリングをO(MN²)からO(MN)に削減。AlphaFold2ベースラインを改善し、特に中程度の信頼度領域で優れています。
#量子アルゴリズム #タンパク質フォールディング #創薬
#量子アルゴリズム #タンパク質フォールディング #創薬
Новый конвейер QAOA с анзацем, сохраняющим ограничения, и инициализацией W-состояния оптимизирует упаковку боковых цепей белков, сокращая масштабирование двухкубитных вентилей с O(MN²) до O(MN). Улучшает результаты относительно базовой модели AlphaFold2, особенно в областях ср...
QAOA-базированная упаковка боковых цепей белков с анзацем, сохраняющим ограничения
arxiv.org
October 8, 2026 at 9:15 AM
Новый конвейер QAOA с анзацем, сохраняющим ограничения, и инициализацией W-состояния оптимизирует упаковку боковых цепей белков, сокращая масштабирование двухкубитных вентилей с O(MN²) до O(MN). Улучшает результаты относительно базовой модели AlphaFold2, особенно в областях ср...
Eine neuartige QAOA-Pipeline mit zwangsbedingungserhaltender Ansatz und W-Zustand-Initialisierung optimiert die Protein-Seitenketten-Packung und reduziert die Zwei-Qubit-Gatter-Skalierung von O(MN²) auf O(MN). Verbessert die AlphaFold2-Baseline, besonders in Regionen mit moder...
QAOA-basierte Protein-Seitenketten-Packung mit zwangsbedingungserhaltender Ansatz
arxiv.org
October 8, 2026 at 9:14 AM
Eine neuartige QAOA-Pipeline mit zwangsbedingungserhaltender Ansatz und W-Zustand-Initialisierung optimiert die Protein-Seitenketten-Packung und reduziert die Zwei-Qubit-Gatter-Skalierung von O(MN²) auf O(MN). Verbessert die AlphaFold2-Baseline, besonders in Regionen mit moder...
Novel QAOA pipeline with constraint-preserving ansatz and W-state initialization optimizes protein sidechain packing, reducing two-qubit gate scaling from O(MN²) to O(MN). Improves upon AlphaFold2 baseline, especially in moderate-confidence regions.
#QuantumAlgorithms #ProteinFolding #DrugDiscovery
#QuantumAlgorithms #ProteinFolding #DrugDiscovery
QAOA-Based Protein Sidechain Packing with Constraint-Preserving Ansatz
arxiv.org
October 8, 2026 at 9:13 AM
Novel QAOA pipeline with constraint-preserving ansatz and W-state initialization optimizes protein sidechain packing, reducing two-qubit gate scaling from O(MN²) to O(MN). Improves upon AlphaFold2 baseline, especially in moderate-confidence regions.
#QuantumAlgorithms #ProteinFolding #DrugDiscovery
#QuantumAlgorithms #ProteinFolding #DrugDiscovery
새로운 QAOA 파이프라인에 제약 조건 보존 앤자츠와 W-상태 초기화를 적용하여 단백질 측쇄 패킹을 최적화하며, 2-큐비트 게이트 스케일링을 O(MN²)에서 O(MN)으로 감소시킵니다. AlphaFold2 기준선을 능가하며, 특히 중간 신뢰도 영역에서 성능을 향상시킵니다.
#양자알고리즘 #단백질폴딩 #신약개발
#양자알고리즘 #단백질폴딩 #신약개발
QAOA 기반 제약 조건 보존 앤자츠를 이용한 단백질 측쇄 패킹
arxiv.org
October 8, 2026 at 9:13 AM
צינור QAOA חדשני עם אנסאץ משמר-אילוצים ואתחול מצב-W מייעל את אריזת שרשראות הצד של חלבון, ומפחית את קנה המידה של שערי שתי-qubit מ-O(MN²) ל-O(MN). משפר בהשוואה ל-baseline של AlphaFold2, במיוחד באזורי ביטחון בינוני.
#אלגוריתמים_קוונטיים #קיפול_חלבון #גילוי_תרופות
#אלגוריתמים_קוונטיים #קיפול_חלבון #גילוי_תרופות
אריזת שרשראות צד חלבונות מבוססת QAOA עם אנסאץ משמר-אילוצים
arxiv.org
October 8, 2026 at 9:16 AM
צינור QAOA חדשני עם אנסאץ משמר-אילוצים ואתחול מצב-W מייעל את אריזת שרשראות הצד של חלבון, ומפחית את קנה המידה של שערי שתי-qubit מ-O(MN²) ל-O(MN). משפר בהשוואה ל-baseline של AlphaFold2, במיוחד באזורי ביטחון בינוני.
#אלגוריתמים_קוונטיים #קיפול_חלבון #גילוי_תרופות
#אלגוריתמים_קוונטיים #קיפול_חלבון #גילוי_תרופות
خط أنابيب QAOA مبتكر يجمع بين ansatz محفوظ للقيود وتهيئة حالة W، ويحسّن تجميع السلاسل الجانبية للبروتين، مما يقلل توسع بوابة الكيوبت المزدوجة من O(MN²) إلى O(MN). يحقق تحسناً مقارنة بخط الأساس AlphaFold2، لا سيما في مناطق الثقة المتوسطة.
#خوارزميات_الكمية #طي_البروتين #اكتشاف_الأدوية
#خوارزميات_الكمية #طي_البروتين #اكتشاف_الأدوية
تجميع السلاسل الجانبية للبروتين باستخدام QAOA مع Ansatz محفوظ للقيود
arxiv.org
October 8, 2026 at 9:16 AM
خط أنابيب QAOA مبتكر يجمع بين ansatz محفوظ للقيود وتهيئة حالة W، ويحسّن تجميع السلاسل الجانبية للبروتين، مما يقلل توسع بوابة الكيوبت المزدوجة من O(MN²) إلى O(MN). يحقق تحسناً مقارنة بخط الأساس AlphaFold2، لا سيما في مناطق الثقة المتوسطة.
#خوارزميات_الكمية #طي_البروتين #اكتشاف_الأدوية
#خوارزميات_الكمية #طي_البروتين #اكتشاف_الأدوية
Nuevo pipeline QAOA con ansatz que preserva restricciones e inicialización de estado W optimiza el empaque de cadenas laterales de proteínas, reduciendo el escalado de puertas de dos qubits de O(MN²) a O(MN). Mejora en comparación con la línea base de AlphaFold2, especialmente...
Empaque de Cadenas Laterales de Proteínas Basado en QAOA con Ansatz que Preserva Restricciones
arxiv.org
October 8, 2026 at 9:14 AM
Nuevo pipeline QAOA con ansatz que preserva restricciones e inicialización de estado W optimiza el empaque de cadenas laterales de proteínas, reduciendo el escalado de puertas de dos qubits de O(MN²) a O(MN). Mejora en comparación con la línea base de AlphaFold2, especialmente...
बाधा-संरक्षणीय ansatz और W-स्थिति आरंभीकरण के साथ नवीन QAOA पाइपलाइन प्रोटीन साइडचेन पैकिंग को अनुकूलित करता है, दो-क्वबिट गेट स्केलिंग को O(MN²) से O(MN) तक कम करता है। AlphaFold2 आधारभूत से बेहतर प्रदर्शन करता है, विशेष रूप से मध्यम-आत्मविश्वास क्षेत्रों में।
QAOA-आधारित प्रोटीन साइडचेन पैकिंग के साथ बाधा-संरक्षणीय Ansatz
arxiv.org
October 8, 2026 at 9:15 AM
बाधा-संरक्षणीय ansatz और W-स्थिति आरंभीकरण के साथ नवीन QAOA पाइपलाइन प्रोटीन साइडचेन पैकिंग को अनुकूलित करता है, दो-क्वबिट गेट स्केलिंग को O(MN²) से O(MN) तक कम करता है। AlphaFold2 आधारभूत से बेहतर प्रदर्शन करता है, विशेष रूप से मध्यम-आत्मविश्वास क्षेत्रों में।
Un pipeline QAOA novateur avec ansatz préservant les contraintes et initialisation d'état W optimise l'empaquetage des chaînes latérales de protéines, réduisant la mise à l'échelle des portes à deux qubits de O(MN²) à O(MN). Améliore par rapport au baseline AlphaFold2, particu...
Empaquetage des chaînes latérales de protéines basé sur QAOA avec ansatz préservant les contraintes
arxiv.org
October 8, 2026 at 9:14 AM
Un pipeline QAOA novateur avec ansatz préservant les contraintes et initialisation d'état W optimise l'empaquetage des chaînes latérales de protéines, réduisant la mise à l'échelle des portes à deux qubits de O(MN²) à O(MN). Améliore par rapport au baseline AlphaFold2, particu...
Pipeline inovador de QAOA com ansatz que preserva restrições e inicialização de estado W otimiza o empacotamento de cadeias laterais de proteínas, reduzindo a escala de portas de dois qubits de O(MN²) para O(MN). Melhora em relação à linha de base do AlphaFold2, especialmente ...
Empacotamento de Cadeias Laterais de Proteínas Baseado em QAOA com Ansatz que Preserva Restrições
arxiv.org
October 8, 2026 at 9:17 AM
Pipeline inovador de QAOA com ansatz que preserva restrições e inicialização de estado W otimiza o empacotamento de cadeias laterais de proteínas, reduzindo a escala de portas de dois qubits de O(MN²) para O(MN). Melhora em relação à linha de base do AlphaFold2, especialmente ...
具有约束保留ansatz和W态初始化的新颖QAOA流程优化蛋白侧链堆积，将双量子门扩展从O(MN²)降低到O(MN)。相比AlphaFold2基线有所改进，特别是在中等置信度区域。
#量子算法 #蛋白质折叠 #药物发现
#量子算法 #蛋白质折叠 #药物发现
基于QAOA的约束保留Ansatz蛋白侧链堆积
arxiv.org
October 8, 2026 at 9:12 AM
一項新穎的QAOA管道，採用保約束Ansatz和W態初始化來優化蛋白質側鏈堆積，將雙量子位門的擴展複雜度從O(MN²)降低到O(MN)。相比AlphaFold2基線有所改進，特別是在中等置信度區域表現更佳。
#量子算法 #蛋白質摺疊 #藥物發現
#量子算法 #蛋白質摺疊 #藥物發現
基於QAOA的保約束Ansatz蛋白質側鏈堆積
arxiv.org
October 8, 2026 at 9:12 AM
Đường ống QAOA mới lạ với ansatz bảo tồn ràng buộc và khởi tạo trạng thái W tối ưu hóa đóng gói chuỗi bên protein, giảm mở rộng cổng hai qubit từ O(MN²) xuống O(MN). Cải thiện so với đường cơ sở AlphaFold2, đặc biệt là trong các vùng độ tin cậy vừa phải.
Đóng Gói Chuỗi Bên Protein Dựa Trên QAOA Với Ansatz Bảo Tồn Ràng Buộc
iq.fp2.dev
October 8, 2026 at 9:16 AM
Đường ống QAOA mới lạ với ansatz bảo tồn ràng buộc và khởi tạo trạng thái W tối ưu hóa đóng gói chuỗi bên protein, giảm mở rộng cổng hai qubit từ O(MN²) xuống O(MN). Cải thiện so với đường cơ sở AlphaFold2, đặc biệt là trong các vùng độ tin cậy vừa phải.
Pipeline QAOA ที่เป็นนวัตกรรมพร้อม Ansatz ที่อนุรักษ์ข้อจำกัดและการเริ่มต้น W-state เพิ่มประสิทธิภาพการบรรจุ Sidechain โปรตีน ลดการปรับขนาด Two-qubit Gate จาก O(MN²) เป็น O(MN) ปรับปรุงจากพื้นฐาน AlphaFold2 โดยเฉพาะในพื้นที่ที่มีความเชื่อมั่นปานกลาง
#อัลกอริทึมควอนตัม #พับโปรตีน #การค้นพบยา
#อัลกอริทึมควอนตัม #พับโปรตีน #การค้นพบยา
การบรรจุ Sidechain โปรตีนโดยใช้ QAOA พร้อม Ansatz ที่อนุรักษ์ข้อจำกัด
arxiv.org
October 8, 2026 at 9:16 AM