Issue8 - Search

Users
Tweets

しゅん @SYUN0209

Jun 15

イエローマガジン ISSUE8 23-24 読み終えました。あぁ、もう２年もたったんですね。そんなに経った感じがしませんでした。サマソニの出演、キュレーションじゃなかったら断っていたというのに驚きました。私もキュレーションじゃなかったら、行かなかったかもと思っていたので。楽しかったです。

10

524

贅沢ミルク @zeitaku1129

Jun 13

issue8のスポーン高いなあ置けなくなったし手放そうか迷うな

30

しゅん @SYUN0209

Jun 10

イエマガISSUE8、170頁まで読みました。特に石橋英子さんの音愛遍歴が面白く、細野晴臣氏の中之島公会堂のライブ帰りに、京都のクラブメトロで、ジム・オルークと石橋英子さんのイベントがあるとのチラシをもらい、行ってきました。ハッキリ言ってよくわからなかったのですが、行ってみて良かったです

1

147

しゅん @SYUN0209

Jun 8

老眼鏡が出来上がって、イエマガ読むことができるようになった。今で40ページ読んだ。全部で400ページなので、このペースで読めば10日で読み終わる。読み終えるのあっという間かも。ちなみにISSUE8の話です。

6

153

ミドリマン☘️@midorimanbb

Jun 7

adidas DON ISSUE8「Spida-Man」

25

981

JCIM & JCTC Journals @JCIM_JCTC

Jun 4

Salt Bridge Builder: Using Residue Distances to Predict Salt Bridge Formation pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #Bioinformatics

Salt Bridge Builder: Using Residue Distances to Predict Salt Bridge Formation

Salt bridges contribute disproportionately to protein folding stability and protein–protein interaction energetics, yet systematic tools for engineering novel salt bridges remain limited. There are...

6

18

922

JCIM & JCTC Journals @JCIM_JCTC

Jun 4

Explainability Methods from Machine Learning Detect Important Drugs’ Atoms in Drug-Target Interactions #MachineLearning pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #Bioinformatics

Explainability Methods from Machine Learning Detect Important Drugs’ Atoms in Drug-Target Interac...

Predicting drug-target interactions (DTI) with graph neural networks (GNNs) is hindered by their lack of interpretability. To address this, we benchmark four explainable artificial intelligence (XAI)...

4

18

904

JCIM & JCTC Journals @JCIM_JCTC

Jun 4

Controllable Protein Design by Prefix-Tuning Protein Language Models pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #Bioinformatics

Controllable Protein Design by Prefix-Tuning Protein Language Models

The design of novel proteins with tailored functionalities presents a transformative approach to addressing pressing biomedical challenges. In this study, we propose PrefixProt, a framework for...

3

9

529

JCIM & JCTC Journals @JCIM_JCTC

Jun 3

DUW-MGCA: A Dynamic Uncertainty-Weighted Multi-Granularity Coattention Framework for Protein–Ligand Interaction Prediction from Hybrid QM/MD Data pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #Bioinformatics

DUW-MGCA: A Dynamic Uncertainty-Weighted Multi-Granularity Coattention Framework for Protein–Ligand...

To bridge the fidelity gap between high-fidelity quantum mechanics (QM) calculations and low-cost, noisy molecular dynamics (MD) trajectories, this paper proposes a dynamic uncertainty-weighted...

7

14

754

JCIM & JCTC Journals @JCIM_JCTC

Jun 3

Biophysical Modeling Elucidates Mechanistic Principles for Rational Molecular Glue Design pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #PharmaceuticalModeling

Biophysical Modeling Elucidates Mechanistic Principles for Rational Molecular Glue Design

Molecular glues are small molecules that offer a powerful strategy to target previously “undruggable” proteins of interest (POI) by enhancing their interactions with other proteins (effectors)....

1

5

604

JCIM & JCTC Journals @JCIM_JCTC

Jun 3

Conformational Dynamics of Na -Pumping NADH-Quinone Oxidoreductase during Na Translocation from AlphaFold-Facilitated Markov State Modeling pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #compchem

Conformational Dynamics of Na -Pumping NADH-Quinone Oxidoreductase during Na Translocation from...

The Na -pumping NADH–quinone oxidoreductase (Na -NQR) is a respiratory chain enzyme found in pathogenic bacteria, including Vibrio cholerae, and is essential for energy metabolism by generating a...

2

12

554

JCIM & JCTC Journals @JCIM_JCTC

Jun 2

High-PepBinder: A pLM-Guided Latent Diffusion Framework for Affinity-Aware Target-Specific Peptide Design pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #compchem

High-PepBinder: A pLM-Guided Latent Diffusion Framework for Affinity-Aware Target-Specific Peptide...

Peptides, as therapeutic molecules, offer unique advantages in targeting complex protein surfaces, yet their rational design remains limited by the vastness of the sequence space and the constraints...

1

15

641

JCIM & JCTC Journals @JCIM_JCTC

Jun 2

SAFR: Enabling Fragment-Based Drug Discovery with a Synthetic Binding Pose Data Set #DrugDiscovery pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #compchem

SAFR: Enabling Fragment-Based Drug Discovery with a Synthetic Binding Pose Data Set

Fragment-Based Drug Discovery (FBDD) is a powerful strategy with a proven track record of generating potent bioactive small molecules from low-affinity chemical fragments. Computational approaches to...

2

7

578

JCIM & JCTC Journals @JCIM_JCTC

Jun 2

Stoichiometric Modeling and Stability Analysis of Synthesis of Alkane Reactions Using PINNs with PDFP Optimization: Applications in Pharmaceutical, Rubber, and Fuel pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #compchem

Stoichiometric Modeling and Stability Analysis of Synthesis of Alkane Reactions Using PINNs with...

In this study, we present a physics-informed neural network for stoichiometric modeling and stability analysis of synthesis of alkane reactions with optimal control, motivated by applications in the...

5

504

JCIM & JCTC Journals @JCIM_JCTC

Jun 2

Lipopolysaccharide–Phospholipid Separation in the Outer Membrane Vesicle Model Promotes Preferential Binding of Antimicrobial Peptides at Lipid Interfaces pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #compchem

Lipopolysaccharide–Phospholipid Separation in the Outer Membrane Vesicle Model Promotes Preferent...

Multidrug-resistant Gram-negative pathogens pose a major global medical challenge due to the lack of new antibiotics. Outer membrane vesicles (OMVs) in Gram-negative bacteria significantly contribute...

2

7

445

JCIM & JCTC Journals @JCIM_JCTC

Jun 1

Heavy Metal Directly Blocks Potassium Channels: An Experimental and Theoretical Approach #MolecularDynamics pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #compchem

Heavy Metal Directly Blocks Potassium Channels: An Experimental and Theoretical Approach

Modeling the interaction of heavy-metal cations with ion channels remains challenging due to their strong electrostatics, complex coordination chemistry, and the need to probe permeation under driven...

1

7

607

JCIM & JCTC Journals @JCIM_JCTC

Jun 1

Mechanism of c-Cbl Transition from Autoinhibited to Partially Open State via Substrate Binding #MolecularDynamics pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #compchem

Mechanism of c-Cbl Transition from Autoinhibited to Partially Open State via Substrate Binding

Cellular Casitas B-lineage lymphoma (c-Cbl), a RING-type E3 ligase, regulates the degradation of diverse proteins, whose dysregulation is implicated in solid tumors and hematological malignancies....

3

10

643

JCIM & JCTC Journals @JCIM_JCTC

Jun 1

The Disordered JM Motif in RTKs Promotes Classical DFGoutConformation Formation via the Dynamic Effect #MolecularDynamics pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #compchem

The Disordered JM Motif in RTKs Promotes Classical DFGout Conformation Formation via the Dynamic...

Receptor tyrosine kinases (RTKs) are validated anticancer targets, and targeting their DFGout conformations represents a mainstream strategy for developing highly selective type II inhibitors. RTKs...

1

3

551

JCIM & JCTC Journals @JCIM_JCTC

May 31

Assessing Molecular Dynamics in Predicting Aptamer–Ligand Binding Thermodynamics: Insights from the OTA Binding Aptamers #MolecularDynamics #Aptamer pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue8 #compchem

Assessing Molecular Dynamics in Predicting Aptamer–Ligand Binding Thermodynamics: Insights from the...

The targeting of nucleic acid platforms is of particular interest in biochemistry and pharmaceutical applications. Among nucleic-based structures, aptamers, short, synthetic oligonucleotides, stand...

5

14

837

JCIM & JCTC Journals @JCIM_JCTC

May 31

Constant-pH Molecular Dynamics of Cationic Peptide Dendrimers Binding to siRNA #MolecularDynamics pubs.acs.org/doi/10.1021/acs… @MiguelMachuque1 #JCIM Vol66 Issue8 #compchem

Constant-pH Molecular Dynamics of Cationic Peptide Dendrimers Binding to siRNA

Transfection, the process of delivering genetic material into eukaryotic cells, is crucial in biotechnology and the development of treatments. Naked nucleic acids face challenges such as enzymatic...

4

24

1,277