Merizo kitchen【jp/en】 twitch.tv/mentsuru
112
AlphaFind v2: Similarity search in AlphaFold DB and TED domains across structural contexts
1 AlphaFind v2 is a web server for fast, structure-based similarity search at AlphaFold DB scale, combining embedding-based prefiltering with alignment-based refinement to keep results biologically interpretable (TM-score/RMSD) while staying interactive.
2 The key design idea is “search across structural contexts”: users can search full chains, restrict comparisons to high-confidence regions using AlphaFold pLDDT thresholds (70/80/90), search TED domains, or run a TED Multidomain mode that captures domain combinations rather than single-domain matches.
3 The workflow is staged for responsiveness: Phase 2 returns immediate approximate kNN results from a vector database (top k=100 by cosine similarity), while Phase 3 runs asynchronously in the background to refine rankings using US-align and report TM-score, RMSD, aligned residues, and interactive superpositions.
4 pLDDT-aware search directly addresses a common AlphaFold-era problem: low-confidence/disordered regions can dominate alignments and hide true homologs. By trimming residues below chosen pLDDT thresholds, AlphaFind v2 focuses similarity on stable structural cores.
5 Domain-level search is integrated via TED: AlphaFind v2 supports direct TED domain retrieval and alignment restricted to domain residue boundaries, enabling more fine-grained detection of shared folds when full-length proteins differ in architecture.
6 TED Multidomain mode targets proteins where function/evolution is encoded in domain composition and order. It aggregates multiple domain-to-domain matches into a single score/alignment, aiming to recover “same architecture” relationships that single-domain hits would miss.
7 A distinctive interface feature in TED Multidomain is interactive weighting: sliders adjust each matched domain pair’s contribution, updating the 3D alignment view to move between (i) inspecting one domain precisely and (ii) assessing global multi-domain arrangement.
8 Under the hood, AlphaFold DB v4 chains are embedded into 1536D vectors using an ESM3-based pipeline; additional embeddings are computed after removing low-confidence residues (pLDDT < 70/80/90). TED domains use precomputed 128D Foldclass embeddings.
9 Engineering choices focus on scalable, low-latency search: OpenSearch vector DB with HNSW (16x compression, on-disk), a Python/Flask REST API, Celery Redis for async refinement jobs, PostgreSQL for state/caching, and Kubernetes for horizontal scaling.
10 Reported benchmarks show rapid retrieval plus strong refinement quality: approximate results in ~2.4 s for chains and ~0.49 s for domains, with refinement completing in tens of seconds; evaluation indicates higher average TM-scores than AlphaFind v1, FoldSeek server (TM computed separately), and Merizo-search (domains), with statistical significance (P < 0.05).
11 Case study (PIN3 auxin carrier): full-chain search struggles due to large disordered loops, but pLDDT ≥ 90 mode finds homologs with TM-score up to 0.947, illustrating how confidence-filtered structural search can recover relationships obscured by structural “noise”.
12 Case study (NCAM1): TED Multidomain mode captures the characteristic Ig-domain fibronectin type III arrangement, helping identify proteins with similar multidomain architecture; interactive reweighting helps resolve cases where domain positions differ across predictions.
📜Paper: doi.org/10.1093/nar/gkag372
#ProteinStructure #AlphaFold #StructuralBioinformatics #ProteinDomains #SimilaritySearch #Embeddings #WebServer #TMscore #CATH #TED #ComputationalBiology
1
6
41
2,635
Apr 10
フィリピン海プレート
4.9
193 km SSW of Merizo Village, Guam
2026 04-10 00:25 50.7km
4.9
Volcano Islands, Japan region
00:49 22.1km
5.1
Izu Islands, Japan region
03:54 10.0km
4.5
185 km SW of Merizo Village, Guam
08:26 10.0km
4.6
Izu Islands, Japan region
11:24 29.8km
4
7
263
4.9 earthquake occurred 193km SSW of Merizo Village, Guam at 15:25 UTC! #earthquake #MerizoVillage earthquak.es/us6000snpr
1
2
117
March 25 Saint Dismas, the "Good Thief"
died 30 AD
Patronage:
prisoners, especially condemned prisoners
undertakers
funeral directors
repentant thieves
Merizo, Guam
San Dimas, Durango
.
Saint Dismas , also known as the “Good Thief” or the “Penitent Thief”, crucified beside Jesus. While Saint Dismas was never officially canonized by the Church, he is considered a saint by virtue of Jesus inviting him into Paradise while on the Cross. Saint Dismas is the patron saint of condemned prisoners, reformed thieves, undertakers, funeral directors, penitent sinners, and prisoners. His life and story provide inspiration for each of us—especially during this Lenten season—on the importance of true repentance.
.
From the Gospel of Luke, the story of Saint Dismas, the Good Thief:
.
39 One of the criminals who hung there hurled insults at him: “Aren’t you the Messiah? Save yourself and us!”
40 But the other criminal rebuked him. “Don’t you fear God,” he said, “since you are under the same sentence? 41 We are punished justly, for we are getting what our deeds deserve. But this man has done nothing wrong.”
42 Then he said, “Jesus, remember me when you come into your kingdom.”
43 Jesus answered him, “Truly I tell you, today you will be with me in paradise.” (Luke 23:39-43)
.
In the Gospel of Saint Luke, we read of the Good Thief’s repentance and humility, and of Jesus’ forgiveness of him. In the apocryphal Gospel of Nicodemus, we learn the name of the Good Thief, Dismas:
.
“And Pilate, after sentence, ordered a title to be written in Hebrew, Greek, and Latin letters, according to what the Jews said: This is the King of the Jews . And one of the robbers who were hanged, by name Gestas, said to Him: If you are the Christ , free yourself and us. And Dismas answering, rebuked him, saying: Do you not even fear God, who art in this condemnation? for we justly and deservedly have received those things which we endure; but He has done no evil. And he kept saying to Jesus: Remember me, Lord, in Your kingdom. And Jesus said to him: Verily I say unto you, that today shall you be with me in paradise.”
.
We know much about the death of Saint Dismas, but little about his early life. What is known derives from a letter written by Saint Anselm, telling what might be the pious legend of Saint Dismas and his companion, Gestas, and their encounter with the Holy Family. From these writings, we are told that Dismas and Gestas were thieves, who set upon the Holy Family—Mary, Joseph, and the infant Jesus—as they fled into Egypt following the massacre of the Holy Innocents. As the thieves advanced upon the unarmed family, Saint Dismas was moved by the “Glorious beauty and majesty” of Jesus, and rather than rob them, defended them against the other brigands. Dismas hosted the Holy Family in his own cave, offering all that he had to them, and upon seeing the respect he paid to her child, Our Blessed Mother assured him that he would be rewarded for his actions prior to his death
.
While Dismas continued in a life of crime following that sacred encounter, although Saint Augustine wondered in his writings if he might also have been baptized into the faith. Regardless, Saint Dismas (according to Saint Anselm) always conserved the memory of that promise, trusting that it would be fulfilled.
.
From the letter of Saint Anselm:
.
"Dismas was living in a forest on the confines of Egypt, when Mary went thither with the Child Jesus, to escape the rage of Herod. He was a highwayman, and the son of the chief of a band of robbers. One day, as he lay in ambush, he saw a man, a young woman, and a little Child approaching, from whom he rightly expected no opposition. Therefore, he went towards them, with his comrades, with the intention to ill-treat them. But he was at once so charmed with the supernatural beauty and grace which shone on the countenance of Jesus, that instead of doing them harm, he gave them hospitality in the cave which he inhabited, and made ready for them everything of which they stood in need. Mary was grateful for the tenderness and care which the robber bestowed on her Beloved Son, and warmly thanking him, she assured him that he would be rewarded before his death. This promise was fulfilled later, when Dismas was crucified with the Savior of the World, and obtained the grace of repentance in his last hour, openly confessing Jesus Christ's Divinity. When the Apostles had fled, he had the happiness to receive the first fruits of the Redeemer's Sacrifice, and soon after, entered the Heavenly Kingdom with his Savior.”
.
Saint Dismas is a symbol of the Lord’s Divine Mercy. He inspires us to trust in the Lord, to recognize our own human weaknesses, and to bring them to Jesus on the Cross—taking full responsibility and accountability for our actions, and offering them in hope to Christ. While Saint Dismas struggled throughout his life, and stumbled in sin, upon the cross he held onto the hope that Our Blessed Mother had provided to him while still a youth—that he would be rewarded for his kindness, obedience, and love of Jesus.
.
So it is with Saint Dismas, and so it is with us, as well. Our loving God has made us the same promise that was made to Dismas, and that promise will be fulfilled. We look toward our heavenly reward with hearts of true repentance, recognizing that our faith in Jesus Christ should always give us that same certain hope that was the good thief's when Jesus said to him: "Today you will be with me in Paradise."
.
Saint Peter of Damascus On True Repentance
.
It is always possible to make a new start by means of repentance. ‘You fell,’ it is written, ‘now arise’ (Proverbs 24:16.) And if you fall again, then rise again, without despairing at all of your salvation, no matter what happens. So long as you do not surrender yourself willingly to the enemy, your patient endurance, combined with self-reproach will suffice for your salvation. ‘For at one time we ourselves went astray in folly and disobedience,’ says St. Paul. ‘…Yet He saved us, not because of any good things we had done, but in His mercy’ (Titus 3:5.) So do not despair in any way, ignoring God’s help, for He can do whatever He wishes. On the contrary, place your hope in Him and He will do one of these things: either through trials or temptations, or in some other way which He alone knows, He will bring about your restoration; or He will accept your patient endurance and humility in the place of works; or because of your hope He will act lovingly towards you in some other way of which you are not aware, and so will save your shackled soul. Only do not abandon your Physician, for otherwise you will suffer senselessly the twofold death because you do not know the hidden ways of God.”
.
Almighty and merciful God, who justify the wicked, we beg You graciously to grant that just as Your Only-begotten Son drew the Blessed Thief to Himself with His kind glance, You might move us also to worthy repentance, and grant also to us as You promised to him the everlasting glory of Paradise. Through the same Lord Jesus Christ who lives and reigns with You and the Holy Spirit, one God, forever and ever. Amen.
.
Glorious Saint Dismas, thou alone of all the great Penitent Saints wert directly canonized by Christ Himself; thou wert assured of a place in Heaven with Him "this day" because of the sincere confession of thy sins to Him in the tribunal of Calvary and thy true sorrow for them as thou hungest beside Him in that open confessional; thou who by the direct sword thrust of thy love and repentance didst open the Heart of Jesus in mercy and forgiveness even before the centurion's spear tore it asunder; thou whose face was closer to that of Jesus in His last agony, to offer Him a word of comfort, closer even than that of His Beloved Mother, Mary; thou who knewest so well how to pray, teach me the words to say to Him to gain pardon and the grace of perseverance; and thou who art so close to Him now in Heaven, as thou wert during His last moments on earth, pray to Him for me that I shall never again desert Him, but that at the close of my life I may hear from Him the words He addressed to you: "This day thou shalt be with Me in Paradise."
.
Eternal Father, I wish to honor St. Dismas, and I give Thee thanks for all the graces Thou hast bestowed upon him. I ask Thee to please increase grace in my soul through the merits of this saint, and I commit the end of my life to him by this special prayer, so that by virtue of Thy goodness and promise, St. Dismas might be my advocate and provide whatever is needed at that hour. Amen.
2
7
139
Metagenomic‑Scale Analysis of the Predicted Protein Structure Universe
1 AFESM combines the AlphaFold Protein Structure Database and the ESM Metagenomic Atlas into an 820‑million‑entry resource, then clusters the data using a two‑step sequence–structure pipeline that reduces redundancy and removes low‑confidence fragments.
2 The clustering yields 5.12 million non‑singleton structural clusters, representing 64.6 % of the total predicted set; 78 % of these clusters are assigned to a single superkingdom, and 83.5 % are not specific to any single biome.
3 Taxonomic labels are predicted for 93 % of cluster members by mapping ESMatlas sequences to GTDB and UniRef90, while biome annotations from MGnify are projected onto clusters to identify environmentally specific structures.
4 Biome‑specific analysis uncovers 1.41 million clusters with at least ten biome annotations; 7.75 % of these are exclusively environmental, revealing distinct structural signatures in extreme habitats such as thermal springs and hypersaline environments.
5 Domain segmentation of ESMatlas chains with Merizo, Chainsaw, and UniDoc, followed by CATH assignment, allows the authors to isolate high‑quality domains and evaluate structural novelty against the existing domain catalogue (TED).
6 Within the 3.2 million ESM‑only non‑singleton cluster representatives, 12 novel domain folds are discovered directly from ESMFold predictions; re‑prediction with ColabFold of previously low‑confidence domains yields an additional 33 novel folds, highlighting the role of prediction quality.
7 Despite the scale of the dataset, genuine fold novelty is sparse: only 0.3 % of ESM‑only clusters contain novel folds, whereas 11,941 unique multi‑domain architectures are identified, underscoring domain recombination as the dominant source of structural innovation.
8 The novel multi‑domain set is enriched for membrane‑associated and transporter domains, and features unexpected pairings such as outer‑membrane beta‑barrels fused to aminotransferase domains, suggesting new functional mechanisms in metagenomic proteins.
9 The study demonstrates that the structural “domain toolbox” is largely saturated across cellular life, but metagenomic data continue to reveal untapped combinations of known folds, providing fertile ground for future functional and evolutionary investigations.
10 The AFESM webserver (afesm.foldseek.com) and the full analysis pipeline are openly available, enabling researchers to explore the integrated protein universe and extend the methodology to multimeric complexes.
💻Code: github.com/steineggerlab/afe…
📜Paper: biorxiv.org/content/10.1101/…
#ProteinStructure #Metagenomics #AlphaFold #ESMFold #DomainInnovation #StructuralBioinformatics #AFESM
5
34
2,411
AlphaFind v2: Similarity Search in AlphaFold DB and TED Domains across Structural Contexts
1 AlphaFind v2 is a web application designed for fast structure-based similarity search in the AlphaFold Database of predicted protein structures, addressing the computational challenges of large-scale 3D structure comparison.
2 It combines fast pre-filtering using protein embeddings that preserve structural information with refinement via US-align, balancing search speed and biological relevance.
3 The tool offers six complementary search modes, including full-protein chain search, pLDDT-filtered searches at 70%, 80%, and 90% thresholds, TED domain search, and TED multidomain search.
4 It supports optional filtering by organism, taxonomy ID, or CATH label, and links search results to corresponding experimental protein structures.
5 The approximate search phase delivers results in seconds, with full structural refinement completed in under a minute on average, outperforming tools like FoldSeek Server and Merizo-search in both speed and average TM-Score.
6 Key applications include identifying homologous proteins in disordered regions via pLDDT filtering and detecting conserved multidomain architectures as demonstrated in case studies of PIN3 and NCAM1 proteins.
7 The web server is built with a Python backend, Flask REST API, Celery asynchronous tasks, OpenSearch vector database, and Kubernetes deployment for scalable performance.
8 AlphaFind v2 uses AlphaFold DB version 4 and precomputed embeddings, with all functionality freely accessible to users without login requirements.
📜Paper: biorxiv.org/content/10.64898…
#AlphaFind #ProteinStructure #StructuralBiology #AlphaFold #Bioinformatics #StructuralSimilarity
7
29
2,284
Feb 23
4.7 magnitude #earthquake. 143 km W of Merizo Village, Guam earthquaketrack.com/quakes/2…
3
1,007
Feb 20
e-QSL recibida de la ultima transmisión de KTWR desde sus transmisores en Merizo en la Isla de Guam Guam. ruquidx.com/qsl-ktwr-ultima-…
3
169
4.5 magnitude #earthquake. 150 km WSW of Merizo Village, Guam earthquaketrack.com/quakes/2…
476
[USGS] M4.5 Feb-09 07:37:12 UTC, 150 km WSW of Merizo Village, Guam, Depth:212.976km, earthquake.usgs.gov/earthqua… #quake
2
4
125
1
467
419
Scriptural Thought for Today:
"You cannot add any time to your life by worrying about it." (Matt. 6:27)
The Biblical word for worry (merimnao) is a compound of two Koine Greek words: "merizo," meaning "to divide," and "nous," which means "the mind." When we worry, it splits our energy between today's priorities and tomorrow's problems. Therefore, part of your mind is on "the now," and the rest is on "the not yet." The result is half-minded living.
Worrying in itself is not a disease, but it causes diseases. It has been connected to high blood pressure, heart trouble, blindness, migraine headaches, thyroid malfunctions, and a host of stomach disorders. Anxiety is an expensive habit. Of course, it might be worth the cost if it worked. Yet, it doesn't! Our frets are futile. Worrying has never brightened a day, solved a problem, or cured a disease.
So, why invest the effort in a practice which fails to produce? Instead, put your trust in the only One who can guide you through life's ups and downs. Next time you start to worry, lean on Christ Jesus for guidance.
#ScripturalThought #NoWorries #TrustInJesus #Matthew6
1
2
17
Major earthquakes hit the world today: (06-01-2026)
➡️ A powerful M5.4 magnitude earthquake hits NE of Port Mathurin, Mauritius 🇲🇺
➡️ A powerful M5.2 magnitude earthquake hits SSW of Merizo Village, Guam 🇬🇺
Source: USGS
TELEGRAM JOIN 👉 t.me/Disasters_World
3
7
534