Seq-Text pair examples

README.md

@@ -90,12 +90,24 @@ python run_PenCL_inference.py \
 The script demonstrates inference using two protein-text pairs from the SwissProt dataset:
 
 **Pair 1:**
-- **Protein Sequence:** MSLEQKKGADIISKILQIQNSIGKTTSPSTLKTKLSEISRKEQENARIQSKL...
-- **Text Description:** PROTEIN NAME: 2' cyclic ADP-D-ribose synthase AbTIR...
+- **Protein Sequence:** <span style="color:red">MAKEDNIEMQGTVLETLPNTMFRVELENGHVVTAHISGKMRKNYIRILTGDKVTVELTPYDLSKGRIVFRSR</span>  
+- **Text Description:** <span style="color:blue">PROTEIN NAME: Translation initiation factor IF-1. FUNCTION: One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit, IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. SUBUNIT: Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. SUBCELLULAR LOCATION: Cytoplasm. SIMILARITY: Belongs to the IF-1 family. LINEAGE: The organism lineage is Bacteria, Pseudomonadota, Gammaproteobacteria, Enterobacterales, Enterobacteriaceae, Escherichia. FAMILY NAMES: Family names are Translation initiation factor 1A / IF-1.</span>
 
 **Pair 2:**
-- **Protein Sequence:** MRFQVIVAAATITMITSYIPGVASQSTSDGDDLFVPVSNFDPKSIFPEIKHP...
-- **Text Description:** PROTEIN NAME: Glucan endo-1,3-beta-D-glucosidase 1...
+- **Protein Sequence:** <span style="color:red">MVKMIVGLGNPGSKYEKTKHNIGFMAIDNIVKNLDVTFTDDKNFKAQIGSTFINHEKVYFVKPTTFMNNSGIAVKALLTYYNIDITDLIVIYDDLDMEVSKLRLRSKGSAGGHNGIKSIIAHIGTQEFNRIKVGIGRPLKGMTVINHVMGQFNTEDNIAISLTLDRVVNAVKFYLQENDFEKTMQKFNG</span>  
+- **Text Description:** <span style="color:blue">PROTEIN NAME: Peptidyl-tRNA hydrolase. FUNCTION: The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. CATALYTIC ACTIVITY: an N-acyl-L-alpha-aminoacyl-tRNA + H2O = a tRNA + an N-acyl-L-amino acid + H(+). SUBUNIT: Monomer. SUBCELLULAR LOCATION: Cytoplasm. SIMILARITY: Belongs to the PTH family. LINEAGE: The organism lineage is Bacteria, Bacillota, Bacilli, Lactobacillales, Streptococcaceae, Streptococcus. FAMILY NAMES: Family names are Peptidyl-tRNA hydrolase.</span>
+
+**Pair 3:**
+- **Protein Sequence:** <span style="color:red">MTDYPIKYRLIKTEKHTGARLGEIITPHGTFPTPMFMPVGTQATVKTQSPEELKAIGSGIILSNTYHLWLRPGDELIARSGGLHKFMNWDQPILTDSGGFQVYSLADSRNITEEGVTFKNHLNGSKMFLSPEKAISIQNNLGSDIMMSFDECPQFYQPYDYVKKSIERTSRWAERGLKAHRRPHDQGLFGIVQGAGFEDLRRQSAADLVAMDFPGYSIGGLAVGESHEEMNAVLDFTTPLLPENKPRYLMGVGAPDSLIDGVIRGVDMFDCVLPTRIARNGTCMTSEGRLVVKNAKFAEDFTPLDHDCDCYTCQNYSRAYIRHLLKADETFGIRLTSYHNLYFLVNLMKKVRQAIMDDNLLEFRQDFLERYGYNKSNRNF</span>  
+- **Text Description:** <span style="color:blue">PROTEIN NAME: Queuine tRNA-ribosyltransferase. FUNCTION: Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)...</span>
+
+**Pair 4:**
+- **Protein Sequence:** <span style="color:red">MAAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIVNEGLKAVAAGMNPMDLKRGIDKAVIAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLEDELDVVEGMQFDRGYLSPYFINKPDTGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLVIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEESAIQGRVAQIRKQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVDDALHATRAAVEEGVVAGGGVALVRVAAKLAGLTGQNEDQNVGIKVALRAMEAPLRQIVSNAGEEPSVVANNVKAGDGNYGYNAATEEYGNMIDFGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKGDAPDLGAAGGMGGMGGMGGMM</span>  
+- **Text Description:** <span style="color:blue">PROTEIN NAME: Chaperonin GroEL. FUNCTION: Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage...</span>
+
+**Pair 5:**
+- **Protein Sequence:** <span style="color:red">MGKAIGIDLGTTNSVVAVVVGGEPVVIPNQEGQRTTPSVVAFTDKGERLVGQVAKRQAITNPENTIFSIKRLMGRKYNSQEVQEAKKRLPYKIVEAPNGDAHVEIMGKRYSPPEISAMILQKLKQAAEDYLGEPVTEAVITVPAYFDDSQRQATKDAGRIAGLNVLRIINEPTAAALAYGLDKKKEEKIAVYDLGGGTFDISILEIGEGVIEVKATNGDTYLGGDDFDIRVMDWLIEEFKKQEGIDLRKDRMALQRLKEAAERAKIELSSAMETEINLPFITADASGPKHLLMKLTRAKLEQLVDDLIQKSLEPCKKALSDAGLSQSQIDEVILVGGQTRTPKVQKVVQDFFGKEPHKGVNPDEVVAVGAAIQAAILKGEVKEVLLLDVTPLSLGIETLGGVFTKIIERNTTIPTKKSQIFTTAADNQTAVTIKVYQGEREMAADNKLLGVFELVGIPPAPRGIPQIEVTFDIDANGILHVSAKDLATGKEQSIRITASSGLSEEEIKKMIREAEAHAEEDRRKKQIAEARNEADNMIYTVEKTLRDMGDRISEDERKRIEEAIEKCRRIKDTSNDVNEIKAAVEELAKASHRVAEELYKKAGASQQGAGSTTQSKKEEDVIEAEVEDKDNK</span>  
+- **Text Description:** <span style="color:blue">PROTEIN NAME: Chaperone protein DnaK. FUNCTION: Acts as a chaperone. INDUCTION: By stress conditions e.g. heat shock...</span>
 
 These pairs demonstrate how the model aligns protein sequences with their corresponding functional descriptions. The model will compute embeddings for both the sequences and descriptions, then calculate their similarities using dot product scores.