Tag: pdb

Proinflammatory chemokine CXCL14 activates MAS-related G protein-coupled receptor MRGPRX2 and its putative mouse ortholog MRGPRB2

Reagents and peptides CXC motif chemokine 14 (CXCL14) was purchased from BIOZOL (Eching, Germany). Proadrenomedullin N-terminal 20 peptide (PAMP-20) was obtained from Tocris Bioscience (Bristol, UK), and cortistatin-14 was from GenScript (NJ, USA). Custom synthesis of CXCL14 analogs was performed by JPT Peptide Technologies (Berlin, Germany) (see Supplementary Fig. 6). Stock…

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eS6 – Ribosomal Proteins

A, 3-D models of human ribosomal subunits based on PDB entries 3J3D and 3J3A (for SSU r-proteins), and on 3J3F and 3J3B (for LSU r-proteins) highlighting the position of individual r-proteins on mature subunits. On small subunits, the 18S rRNA is shown in grey; on large subunits, the 5S, 5.8S…

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Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide | Virology Journal

Analysis of the multisegmented nature of BcssDV1 genome B. cinerea field isolates were previously obtained from infected grapes of vineyards of Italy and Spain and their mycovirome was determined [8]. A new ssDNA virus (BcssDV1, Genbank accession no. MN625247) was discovered and characterized. The sequence previously characterized of BcssDV1 (from…

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Frontiers Publishing Partnerships | Construction of recombinant adenovirus-5 vector to prevent replication-competent adenovirus occurrence

Introduction In recent years, recombinant adenoviral vectors have been used in different fields of biomedical sciences such as in vitro and in vivo gene transfer, vaccine development, and gene therapy (Russell, 2000; Mitani and Kubo, 2002). Multiple features of recombinant adenoviral vectors such as high packaging capacity for transgene insertion,…

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Lipid vesicle(CHARMM Gui files) simulation in GROMACS – User discussions

GROMACS version: 2022.1 and 2020GROMACS modification: Yes/NoHere post your questionHello, I am trying to simulate Lipid based vesicle in GROMACS on Frontera super-computer. The following command I am using to run the simulation. But I am getting error messages. Since I am new I don’t understand the error message perfectly….

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A Database of RNA Modifications

Modomics – A Database of RNA Modifications RsmA from Thermus thermophilus – protein summary. ID Card: Full name: Ribosomal RNA small subunit methyltransferase A Synonym: KsgA, TTHA0083 GI: 55980052 COG: COG0030 UniProt: Q5SM60 Structures: | 3FUT | 3FUU | 3FUW | 3FUV | 3FUX | Enzyme type: methyltransferase Position of…

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TWAS revealed significant causal loci for milk production and its composition in Murrah buffaloes

Cao, C. et al. Power analysis of transcriptome-wide association study: Implications for practical protocol choice. PLoS Genet. 17(2), e1009405 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  De Camargo, G. M. F. et al. Prospecting major genes in dairy buffaloes. BMC Genomics 16, 1–14 (2015). Article  Google Scholar  El-Halawany, N….

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Simulating Histidine Protonation in GROMACS – Beginner Seeking Guidance – User discussions

Hello GROMACS community, I am a total beginner in using GROMACS, and I’m currently working on a project where I need to simulate the protonation state change of histidine residues in a protein, specifically to simulate an acidic environment where histidines gain a proton (NH3+). I have downloaded a protein…

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The initial estimative of -nt parameter – User discussions

GROMACS version: 2022.6GROMACS modification: NoHi, community.I would like to know, how gromacs calculate an initial estimate for number of threads used on mdrun? For example, when run this command “gmx mdrun -deffnm md_0_1 -nb gpu” , for system 1, i can see all my 24 threads been using. Nonetheless, when…

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Q&A Report from the workshop_ _Exploring EMBL-EBI sequence analysis tools and managing bioinformatics workflows | PDF | Sequence Alignment

  Q&A Report from the workshop: QuestonWha is he bes msa ool?clusal 2 and clusal omega are he sameHow would we ener multple sequences? because here is only one inpu boxCould he legend explaining symbiols (*, -,…) be shown in he resul window?Wha is he max number of sequences one…

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Evolution of lysine-specific demethylase 1 and REST corepressor gene families and their molecular interaction

The RCOR gene repertoire expanded in the ancestor of jawed vertebrates To understand the duplicative history of the RCOR genes, we reconstructed gene phylogenies with different taxonomic samplings. The first analysis aimed to understand the evolution of RCOR genes in vertebrates (Fig. 2), whereas in the second, our sampling effort included…

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Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking

Prediction with AlphaFold2 and AlphaFold-Multimer For each PDB the release date in the Protein Data Bank34 was recorded. AlphaFold 2 (2.2.2) was run setting the –max_template_date flag to be the day before the release date of the PDB and the –model_preset to be either monomer for AF or multimer for…

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LP pseudo-atom is not supported

Hi, I want to perform MMPBSA for complex file Command: gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv Error: [INFO ] Starting gmx_MMPBSA v1.6.2 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1…

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dashed PDB file/OXT residues

I think it is clear what is going on once you do a few things. Download and read the header of the PDB file for 3odu: HEADER SIGNALING PROTEIN, HYDROLASE 11-AUG-10 3ODU TITLE THE 2.5 A STRUCTURE OF THE CXCR4 CHEMOKINE RECEPTOR IN COMPLEX WITH TITLE 2 SMALL MOLECULE ANTAGONIST…

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Query about Atom Index Ordering in GROMACS 2021.0 and 2023.3 – Developers discussions

Lorien December 12, 2023, 10:55am 1 Hello. I am developing a constraint algorithm and primarily working with GROMACS 2021.0. In executions without domain decomposition and with constraints set to all-bonds, the atom indices appear to follow an order similar to that in the PDB file. For instance, in simulations involving…

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Energy Minimization while Simulating Supercapacitor Electrode using Constant Charge Method – LAMMPS General Discussion

Hello lammps users, I am new to lammps. I have a system with around 40000 atoms built by assembling two systems: NaCl electrolyte and crumpled graphene electrode. I have made electrolyte using avogadro and packmol, converted pdb to lammps data file using openbabel. I have made graphene sheet using Gopy…

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Command to run gromacs in parallel – User discussions

cjbraz December 11, 2023, 5:06pm 1 GROMACS version: 2023.2GROMACS modification: Yes/NoHere post your question Hello all. I have used CHARMM-GUI solvent builder to print out a script I can use in a protein simulation. I am able to run the script successfully, but would like to run the full script…

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Solved 1. Give one of AlphaFold’s limitations in structure

Transcribed image text: 1. Give one of AlphaFold’s limitations in structure prediction. ( 20% ) 2. Give ONE example of intrinsically disordered proteins’ functional advantages. (20 %) 3. Please use the VSL2 algorithm in PONDR to predict the sequence disorder level of human’s TDP-43 (search it from UniProt). (Please show…

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Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath

Bacterial strains We used P. putida strains S12, DOT-T1E, F1 (kindly gifted by Grant Rybnicky), ATCC 12633 (purchased from ATCC), JUb85 (kindly provided by Samuel Buck), EM383 (kindly gifted by Huseyin Tas), p106 (kindly provided by Carey-Ann Burnham), and KT2440 (obtained from lab stocks). An overnight culture of each P….

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Gromacs 2023.3 on Apple M3 chip – User discussions

GROMACS version: 2023.3GROMACS modification: No Hi folks I know that there have been several threads on running Gromacs with Apple M1 and M1 or M2 chips (e.g. Error compiling Gromacs 2023’s checks on Mac M2), but I recently got a MacBook Pro with the M3 chip, so I was interested…

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New Symmetry Annotation Feature for Macromolecular Assemblies

In an effort to improve the understanding of the structure and function of macromolecular assemblies, a new feature has been introduced to annotate and display symmetry in these structures. This new process, powered by Ananas, provides global symmetry data for each new assembly on a weekly basis. This underlying data…

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Charmm36-jul2022.ff – User discussions – GROMACS forums

GROMACS version:GROMACS modification: Yes/NoHere post your question I am trying to generate amylin 2L86.top using CHARMM36-jul2022.ff and TIP3P. Amylin has 37 residues but the last NH2 is considered as residue 38. Although AMBERsb-star-ILDN.ff works with 38 resiues”, Charmm36-jul2022 does not work (see below):Fatal error:Residue type ‘NH2’ not found in residue…

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GROMACS MD Simulation – proteomics

I received this error when using the GROMACS initial setup tool WARNING: No ICDs were found. Either, Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or Make your system-wide implementation visible by installing ocl-icd-system conda package. jennaj December 7, 2023, 9:27pm 2 Hi @Vibha_Rao That is…

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Gromacs distance calculation between multiple atoms, is it real? – User discussions

rufus December 6, 2023, 8:34pm 1 GROMACS version: 2022GROMACS modification: No Dear all, I have to analyze the trajectory and calculate all distances between a group of atoms (each separate one) and all the surrounding waters, which were at the distance cutoff < 0.35. There were times, when I used…

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cuda sample build fails on windows with CUDA 12.3, VS 2022

When I tries to build cuda bandwidth test sample, MSB3721 error occurs. MSB3721 “”C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v12.3\bin\nvcc.exe” – gencode=arch=compute_50,code=\”sm_50,compute_50\” – gencode=arch=compute_52,code=\”sm_52,compute_52\” – gencode=arch=compute_60,code=\”sm_60,compute_60\” – gencode=arch=compute_61,code=\”sm_61,compute_61\” – gencode=arch=compute_70,code=\”sm_70,compute_70\” – gencode=arch=compute_75,code=\”sm_75,compute_75\” – gencode=arch=compute_80,code=\”sm_80,compute_80\” – gencode=arch=compute_86,code=\”sm_86,compute_86\” – gencode=arch=compute_89,code=\”sm_89,compute_89\” – gencode=arch=compute_90,code=\”sm_90,compute_90\” –use-local-env – ccbin “C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.38.33130\bin\HostX64\x64” -x cu -I./ -I../../../Common -I./…

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Zea mays genotype influences microbial and viral rhizobiome community structure

Oburger E, Schmidt H. New methods to unravel rhizosphere processes. Trends Plant Sci. 2016;21:243–55. Article  CAS  PubMed  Google Scholar  Rout ME, Southworth D. The root microbiome influences scales from molecules to ecosystems: the unseen majority. Am J Bot. 2013;100:1689–91. Article  PubMed  Google Scholar  Pratama AA, Terpstra J, de Oliveria ALM,…

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BioPython | Oxford Protein Informatics Group

Pandas is one of the most used packages for data analysis in python. The library provides functionalities that allow to perfrom complex data manipulation operations in a few lines of code. However, as the number of functions provided is huge, it is impossible to keep track of all of them….

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PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank

While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we present PDBe CCDUtils, a versatile toolkit for processing and analysing small molecules from the PDB in PDBx/mmCIF…

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PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank | Journal of Cheminformatics

The Protein Data Bank (PDB) [1], managed by the worldwide PDB (wwPDB) consortium [2], serves as the single global repository for information on 3D structures of proteins, nucleic acids, and complex assemblies. With over 200,000 entries as of July 2023, about 75% of these structures contain at least one small…

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Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning

Overview of the method DeepAssembly is designed to automatically construct multi-domain protein or complex structure through inter-domain interactions from deep learning. Figure 1 shows an overview of the DeepAssembly protocol. Starting from the input sequence of multi-domain protein (or protein complex), DeepAssembly first generates multiple sequence alignments (MSAs) from genetic databases…

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AutoDock Vina 1.2.0: new docking methods, expanded force field, and Python bindings

J Chem Inf Model. Author manuscript; available in PMC 2023 Nov 28. Published in final edited form as: PMCID: PMC10683950 NIHMSID: NIHMS1947068 Jerome Eberhardt aDepartment of Integrative Structural and Computational Biology, Scripps Research, La Jolla, 92037, California, USA Diogo Santos-Martins aDepartment of Integrative Structural and Computational Biology, Scripps Research, La…

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A Reliable Method for Quantifying Plasma Cell-Free DNA Using an Internal Standard Strategy: Evaluation in a Cohort of Non-Pregnant and Pregnant Women

Martignano F. Cell-free DNA: an overview of sample types and isolation procedures. In: Casadio V, Salvi S, editors. Cell-free DNA as diagnostic markers. Methods in molecular biology, Vol. 1909. New York, NY: Humana Press; 2019. p. 13–27. doi.org/10.1007/978-1-4939-8973-7_2. Volckmar AL, Sültmann H, Riediger A, Fioretos T, Schirmacher P, Endris V,…

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Bacteriophage-host Interactions In Microgravity Onboard The International Space Station

Deep Mutational Scanning profiles beneficial substitutions in the RBP tip domain (A-B) Heatmaps showing normalized functional scores (FN) of all substitutions (red gradient) and wildtype amino acids (FN=1 and black dot upper left) at every position after incubation with E. coli BL21 in (A) microgravity and (B) after terrestrial incubation….

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Computational and bioinformatics tools for life sciences

In recent decades, the development of computational and bioinformatics tools and websites for life sciences has increased exponentially. This great development has gone hand in hand with the availability of genome, proteome and macromolecule structure databases, and also of functional experiments, including microarray and RNAseq expression data, RNA-protein interactions, ChIP-seq,…

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KEGG T01001: 1474

Entry 1474              CDS       T01001                                  Symbol CST6, ECTD15 Name (RefSeq) cystatin E/M   KO K13902   cystatin-M Organism hsa  Homo sapiens (human) Disease H00651   Hypohidrotic ectodermal dysplasia Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:hsa01002]    1474 (CST6)Peptidases and inhibitors [BR:hsa01002] Peptidase inhibitors  Family I25: cystatin family   1474 (CST6) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…

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KEGG T01001: 637

Entry 637               CDS       T01001                                  Symbol BID, FP497 Name (RefSeq) BH3 interacting domain death agonist   KO K04726   BH3 interacting domain death agonist Organism hsa  Homo sapiens (human) Pathway hsa01524   Platinum drug resistance hsa04071   Sphingolipid signaling pathway hsa04115   p53 signaling pathway hsa04210   Apoptosis hsa04215   Apoptosis – multiple species hsa04217   Necroptosis hsa04650   Natural killer cell mediated…

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Python Tools for Genomic Data Analysis: From Sequences to Structures | by Bao Tram Duong | Nov, 2023

Analyzing genomic data, from sequences to structures, is a critical aspect of bioinformatics. Python has a rich ecosystem of tools and libraries specifically designed for genomic data analysis. Here’s an overview of key tools and libraries for various stages of genomic data analysis: Description: Biopython is a comprehensive open-source collection…

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Bioinformatics Programming with Biopython: Advanced Biopython Techniques for Computational Biology | by Bao Tram Duong | Nov, 2023

Biopython is an open-source collection of Python tools for computational biology and bioinformatics. It provides modules and classes to work with biological data such as DNA, RNA, protein sequences, structures, and more. Biopython aims to make it easy for developers to access and manipulate biological data in a programmatic way….

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New study validates AlphaFold2 for predicting mutation effects in proteins

Proteins, the workhorses of biology, are encoded by DNA sequences and are responsible for vital functions within cells. Since the first experimental measurement of a protein structure was made by John Kendrew in the 1950s, protein’s ability to fold into complex three-dimensional structures has long been a subject of scientific…

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Creating a .pdb file from .cml file – User discussions

jankac November 23, 2023, 11:32am 1 GROMACS version: 2023.3GROMACS modification: NoHi everyone!I’m really new to the gromacs and I’m trying to create my first input. The molecule I want to use is a peptide I’m researching. I created a model of my molecule in Avogadro and then converted it to…

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wwPDB News – Deprecation of FTP File Download Protocol in the PDB Archive

The FTP protocol for file downloads has been losing popularity over the years in favor of HTTP/S. There are many advantages of HTTP/S including speed, statelessness, security (HTTPS), and better support. Importantly during the past 2-3 years the main web browsers (Chrome and Firefox) have dropped support for the FTP…

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How to do the MD simulation of a metalloenzyme with ligand? – User discussions

GROMACS version: 2023GROMACS modification: YesHere post your question : Recently, I want to make the simulation of a metalloenzyme with ligand. The metalloenzyme has two Mn ions in its active site. When producing the topol file for this metalloenzyme, gromacs cannot find the Mn ion in the rtp file. I…

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Testing the limits of AlphaFold2’s accuracy in predicting protein structure

Figure 1. A: Overlaid wild-type (grey) and mutant (color), experimental (orange), and predicted (blue) structures of H-NOX protein. B: Wild-type protein with residues colored by strain (a measure of structural deformation), Si; the location of the mutation (residue 71 is mutated from alanine (A) to glycine (G)) is indicated. C:…

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EMDB < EMD-14025

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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EMDB < EMD-16930

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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CHEM271 Genbank – CHEM 271 WINTER 2016 GENBANK ASSIGNMENT Name: ID#: Please answer the questions on

CHEM 271 WINTER 2016 GENBANK ASSIGNMENT Name: ID#: Please answer the questions on this page ONLY, including the back, when necessary 1. Alpha-1 antitrypsin from what organism is defined by accession number NP_001121179.1? Organism: Homo Sapiens 2. How many amino acids does accession number NP_001121179.1 have? The accession number contains…

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wwPDB News – Backbone Annotation and Standardization of Peptide Residues is Now Live

The wwPDB has rolled out updated Chemical Component Dictionary (CCD) data files with standardized atom naming and additional annotation of protein backbone and terminal atoms within peptide residues. Entries containing those updated CCDs have been updated accordingly. This improves the Findability and Interoperability of the PDB data and opens up…

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What AlphaFold tells us about cohesin’s retention on and release from chromosomes

If ATP-dependent dissociation of Scc1’s NTD from the Smc3 neck is a feature intrinsic to Smc-kleisin trimers, then how might Wapl enhance this process? To address this, we used AF to explore how Wapl is first recruited to cohesin and second what effect it has on the configuration of cohesin’s…

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How to correct the position of my primers

I have been having issue getting my primers to match the expected output. For instance the bases of the first primer starting on the left are off by 4 base pairs to the right of the correct position. This is what I am suppose to get: ttggcagttgggaccgttta This is what…

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Using Primer3 with python to genotype a SNP at a particular position

I’m trying to figure out how to genotype an SNP at a particular position. Honestly I’m not sure what that means, but here are the instructions: “The idea is that the user wants to genotype a SNP at a particular position. To do this they will need to amplify a…

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Compare similarity of protein variants

Compare similarity of protein variants 0 I have some .pdb files with structures of variants of the same protein and I’m looking for a way to quantify how similar (or dissimilar) they are from a reference protein. I’ve tried superimposing them and calculating RMSD with ChimeraX or PyMol, the problem…

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Simulated ligand with weird geometries on start.pdb(dump=0) and md_0_100.gro files – User discussions

GROMACS version:2021.4-UbuntuGROMACS modification: Yes/NoHere post your question: I run 100nsec simulation with all ‘default’ parameter suggested by the tutorial Protein-Ligand Complex. After 10 days the simulation was finally over. To visualize the results prior to the analysis step, i uploaded into Pymol start.pdb(dump0) and md_0_100.gro. What I saw was that…

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How do I print out the energy of solute from edr file? – User discussions

pinoji1 November 14, 2023, 8:35pm 1 GROMACS version:2023.3GROMACS modification: NoHow do I print out the energy of solute during the production run in alchemical transformation? I triedgmx energy -f myfile.edr -n myfile.ndx -o solE.xvgBut -n option is not available. Is there any other way to access this information during alchemical…

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RCSB PDB – 8PBD: RAD51 filament on dsDNA bound by the BRCA2 c-terminus

ATPQuery on ATP Download Ideal Coordinates CCD File&nbsp CA [auth C]FA [auth D]IA [auth E]LA [auth F]OA [auth G] CA [auth C],FA [auth D],IA [auth E],LA [auth F],OA [auth G],RA [auth H],UA [auth I],V [auth A],XA [auth J],Z [auth B] Less ADENOSINE-5′-TRIPHOSPHATEC10 H16 N5 O13 P3ZKHQWZAMYRWXGA-KQYNXXCUSA-N CAQuery on CA Download…

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Inhibition of providencia vermicola FabD

Introduction Microbial resistance has become a problem in the contemporary medical environment due to the inadequate development of new antibiotics and the asinine prescription of antibiotics in both developed and developing nations. Antimicrobial resistance (AMR), which affects wealthy and developing nations, is a global concern.1 AMR is a problem for…

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Impact of N221S missense mutation in human ribonucleotide reductase small subunit b on mitochondrial DNA depletion syndrome

hRRM2B mutagenesis study The fatal consequences of N221S mutation7 led to a thorough investigation of the impacts of N221 side chain, a conserved residue in RNR small subunit. Site-directed mutagenesis studies involving six N221 constructs were performed to elucidate the molecular mechanism of N221S related MDDS. The mutations were designed…

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KEGG T01001: 257194

Entry 257194            CDS       T01001                                  Symbol NEGR1, DMML2433, IGLON4, KILON, Ntra Name (RefSeq) neuronal growth regulator 1   KO K06775   neuronal growth regulator 1 Organism hsa  Homo sapiens (human) Pathway hsa04514   Cell adhesion molecules Brite KEGG Orthology (KO) [BR:hsa00001] 09130 Environmental Information Processing  09133 Signaling molecules and interaction   04514 Cell adhesion molecules    257194 (NEGR1) 09180 Brite Hierarchies  09183 Protein families: signaling…

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ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era | Nucleic Acids Research

Abstract ChannelsDB 2.0 is an updated database providing structural information about the position, geometry and physicochemical properties of protein channels—tunnels and pores—within deposited biomacromolecular structures from PDB and AlphaFoldDB databases. The newly deposited information originated from several sources. Firstly, we included data calculated using a popular CAVER tool to complement…

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When will RNA get its AlphaFold moment? | Nucleic Acids Research

Abstract The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches….

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Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

The comparison between MULTICOM servers and other CASP15 server assembly predictors According to the CASP15 official assessment (see the official ranking predictioncenter.org/casp15/zscores_multimer.cgi), MULTICOM_qa and MULTICOM_deep servers ranked 3rd and 5th among all CASP15 assembly server predictors. The MULTICOM human predictors (MULTICOM_human and MULTICOM) ranked 7th and 10th among all CASP15…

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In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data | BMC Genomics

Bentes B, Martinelli J, Souza L, Cavalcante D, Almeida M, Isaac V. Spatial distribution of the amazon river prawn Macrobrachium Amazonicum (Heller, 1862) (Decapoda, Caridea, Palaemonidae) in two perennial creeks of an estuary on the northern coast of Brazil (Guajará Bay, Belém, Pará). Brazilian J Biol. 2011;71:925–35. Article  Google Scholar …

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Integrated AlphaFold based protein modeling and virtual high throughput screening (vHTS) approach for hit generation and target discovery | Poster Board #1602

Virtual high throughput screening (vHTS) has been widely used in AgChem lead discovery to generate new hits. However, in AgChem (fungi, insects, and weeds), high-quality homology models are difficult to build for most essential proteins due to a lack of acceptable templates in PDB database. AlphaFold 2.0 developed by DeepMind,…

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[ atomtypes ] error – User discussions

GROMACS version:GROMACS modification: Yes/NoI want to simulate two types of small molecules in the system, and each type there are multiple of them.I created the files.itp for ligand1 and ligand2 Acpype Server serverThe question I have is this: since there are two types of molecules, can I have two itp…

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EMDB < Search results

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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Rapid in situ RNA imaging based on Cas12a thrusting strand displacement reaction | Nucleic Acids Research

Abstract RNA In situ imaging through DNA self-assembly is advantaged in illustrating its structures and functions with high-resolution, while the limited reaction efficiency and time-consuming operation hinder its clinical application. Here, we first proposed a new strand displacement reaction (SDR) model (Cas12a thrusting SDR, CtSDR), in which Cas12a could overcome…

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Coenzyme-Protein Interactions Since Early Life

Origin & Evolution of Life Status Report biorxiv November 6, 2023 Workflow of this study. All available coenzymes in the PDB were identified according to the CoFactor database (Fischer et al., 2010). The PDB entries of structures bound to coenzymes were downloaded programmatically through the PDBe REST API (pdbe.org/api), including…

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Genome Browser Chimera Interface

Download Chimera Configure for automatic launch in web browsers UCSF Chimera is an interactive molecular modeling system that supports 3-D visualization of protein structures.It runs as an application on the user’s computer. The UCSC Genome Browser provides links to launch Chimera as a helper application for proteins with solved structures…

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The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3

Statistics and reproducibility Anti-AMP IP for LC-MS/MS analysis was performed in three independent biological replicates (n = 3). TSA assay data represents technical triplicates. Time-resolved (de)AMPylation analyzed by LC-MS was performed as biological triplicates. CD measurements were performed in technical triplicates. Anisotropy data is shown as technical triplicates. Anisotropy measurements were repeated…

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Biopython: Empowering Biologists with Computational Tools | by Everton Gomede, PhD | Nov, 2023

Introduction In the realm of modern biology, data analysis and computational techniques have become indispensable for researchers to extract valuable insights from the vast amount of biological data generated today. Biopython is a powerful and versatile open-source software library designed to meet the computational needs of biologists and bioinformaticians. This…

Continue Reading Biopython: Empowering Biologists with Computational Tools | by Everton Gomede, PhD | Nov, 2023

Will Alphabet Achieve With Isomorphic Labs What It Couldn’t With DeepMind?

In 2018, when DeepMind unveiled AlphaFold to the public, a pivotal discovery in medical technology that could predict single-chain protein structures, it disrupted biology, giving new direction to structural biology, in particular.  Two years later, DeepMind announced AlphaFold 2, which cracked half-a-century-old puzzle of protein folding, a defining moment for…

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Reduce PDB doesn’t match Topology File atom – User discussions

GROMACS version: 2023.2GROMACS modification: No I am testing running proteins with mutations through AlphaFold and then passing the PDBs to gromacs to run relaxation. I originally attempted to run this without reducing the molecule, but that definitely didn’t work. Next, I reduced the structure using GitHub – rlabduke/reduce: Reduce –…

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The latest AlphaFold model now covers a variety of biological molecules

The protein folding problem, or at least one of its iterations, consists of reliably determining the 3D structure of a protein from the sequence of its amino acids alone. There is a variety of amino acids serving different purposes, the best known of these molecules being the 22 proteinogenic (protein-creating)…

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Solved Part 2: UniProtKB/SwissProt and Protein Data Bank

Transcribed image text: Part 2: UniProtKB/SwissProt and Protein Data Bank Analysis on SARS-CoV-2 Non-Structural Proteins Objective: Explore the structures, functions, and interactions of SARS-CoV-2 non-structural proteins using resources from UniProtKB/SwissProt and the Protein Data Bank, 1) Visit the PDB resource on SARS-CoV-2 proteins and select a non-structural protein (e.g., NSP3,…

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Pdist pytorch [HFOHSNLLOQ]

Pdist pytorch [HFOHSNLLOQ] Pdist pytorch Based on Torch, PyTorch has become a powerful machine…

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Glycoengineered keratinocyte library reveals essential functions of specific glycans for all stages of HSV-1 infection

Generation of a glycogene knock out library in HaCaT keratinocytes HaCaT is a human keratinocyte cell line capable of forming a stratified squamous epithelium, and thus allows evaluating the infection of the skin tropic HSV-1 in both cell and organotypic tissue culture. In order to address the role of specific…

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Tom Terwilliger Publishes Work on AlphaFold Predictions

Tom Terwilliger Publishes Work on AlphaFold Predictions Tom Terwilliger, a New Mexico Consortium Senior Research Scientist and Los Alamos National Laboratory Scientist, recently published his work, AlphaFold predictions are valuable hypotheses, and accelerate but do not replace experimental structure determination, in bioRxiv, The Preprint Server for Biology. Artificial Intelligence (AI)-based…

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Unraveling the Mysteries: Large Language Models and AlphaFold in Action | by Yadi Shahryary | Nov, 2023

generated by Dall-E 3 In my previous post, I introduced you to the fascinating world of data science, highlighting my journey and the diverse skill set that I bring to the table. Today, let’s dive deeper into two specific areas that are close to my heart and pivotal in the…

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DMS MaPSeq demonstrates perturbations in rRNA folding arising from the Ltv1_L216S mutation.

(A) Secondary structure of 18S rRNA demonstrating residues significantly altered in ribosomes from Ltv1_L216S cells. All residues (except C191) are more accessible in ribosomes from Ltv1_L216S. The extent of the alteration is indicated by yellow, orange or red circles. (B) Residues significantly altered in ribosomes from Ltv1_L216S cells mapped onto…

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DeepMind’s AlphaFold AI Model: Revolutionizing Drug Discovery

DeepMind, a subsidiary of Google, has unveiled its latest iteration of the AlphaFold AI model, promising unprecedented accuracy in predicting molecular structures and interactions. By expanding its capabilities beyond proteins, this groundbreaking development has the potential to revolutionize the field of drug discovery and scientific research. Last year, DeepMind made…

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Gromacs. One or more water molecules can not be settled during minimization – User discussions

Nik November 1, 2023, 10:51am 1 GROMACS version: 2023.1GROMACS modification: NoDuring minimization in Gromacs of the protein molecule (standard procedure for protein without any ligands) I get notification after 13th step:[One or more water molecules can not be settledCheck for bad contacts and/or reduce the timestep if appropriate.Wrote pdb files…

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New molecular insights on medical cannabis

A study explores some key biological mechanisms that help explain the therapeutic effects of medicinal cannabis on inflammation and other disease states. Here, researchers from the European Molecular Biology Laboratory outline their investigations into the effect of tetrahydrocannabinol (THC) on the enzyme Autotaxin. Autotaxin (ATX) is a 99-125 kDa lysophospholipase…

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Google Deepmind shows the next generation of AlphaFold

Summary In a new study, Deepmind and colleagues at Isomorphic Labs show early results from a new version of AlphaFold that brings fully automated structure prediction of biological molecules closer to reality. The Google Deepmind AlphaFold and Isomorphic Labs team today unveiled the latest AlphaFold model. According to the companies,…

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Google’s AI Could Soon Help Design Personalized Drugs to Treat Disease

Google’s artificial intelligence division DeepMind said its AI tool AlphaFold can now predict nearly all the molecules in the Protein Data Bank (PDB), the world’s largest open access database of biological molecules. The breakthrough could help AlphaFold herald in a new era of drug discovery and a massive leap in…

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Google Teases Next Generation of AlphaFold, Expanding AI Structure Prediction Beyond Proteins

In 2020, DeepMind’s AlphaFold AI system shocked researchers by predicting protein structures with unprecedented accuracy. Now, Google and biotech startup Isomorphic Labs have previewed AlphaFold’s next generation, showing dramatically expanded capabilities beyond proteins to model complexes containing DNA, RNA, small molecule ligands, and post-translational modifications (PTMs). This progress solidifies AlphaFold…

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A glimpse of the next generation of AlphaFold

Progress update: Our latest AlphaFold model shows significantly improved accuracy and expands coverage beyond proteins to other biological molecules, including ligands ‍ Since its release in 2020, AlphaFold has revolutionised how proteins and their interactions are understood. Isomorphic Labs and Google DeepMind have been working together to build the foundations…

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Google DeepMind, Isomorphic Labs Unveil Next Generation of AlphaFold

In collaboration with the AI-powered drug discovery company Isomorphic Labs, Google DeepMind has released a new iteration of the protein structure prediction model, AlphaFold 2. The latest model can predict structures for most molecules in the Protein Data Bank (PDB) with high accuracy, often reaching atomic precision, in various important…

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EMDB < EMD-40454

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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AlphaFold model used for docking? and it is ggod?

AlphaFold, an artificial intelligence-based protein structure prediction method, has been evaluated for its accuracy in docking-based drug discovery. The performance of AlphaFold (AF) models in high-throughput docking (HTD) was compared to experimental PDB structures using various docking programs and consensus techniques. The results consistently showed that AF models had worse…

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Transgenic expression in zebrafish embryos with an intact chorion by electroporation and microinjection

Biotechnol Rep (Amst). 2023 Dec; 40: e00814. Nusrat Tazin aDepartment of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA Christopher Jordon Lambert bDepartment of Mechanical Engineering, University of Utah, Salt Lake City, Utah, USA Raheel Samuel bDepartment of Mechanical Engineering, University of Utah, Salt Lake City,…

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Comment: Map genome positions onto protein coordinates?

You need to get the geneID first. For PDB structures, you may be able to retrieve it from RCSB PDB APIs. For AlphaFold UniProt IDs, you can do this way: `url = “rest.uniprot.org/uniprotkb/search?format=json&fields=xref_geneid,gene_names&query=&#8221; + structure; let geneData = await me.getAjaxPromise(url, ‘json’); let geneId = (geneData.results[0] && geneData.results[0].uniProtKBCrossReferences && geneData.results[0].uniProtKBCrossReferences[0]) ?…

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Topological links in predicted protein complex structures reveal limitations of AlphaFold

Identification of topological links in protein complexes To demonstrate why new algorithms are needed to identify topological links in protein‒protein complex structures, we applied existing methods to 4 structures predicted by AlphaFold-Multimer v2.2.0 (Fig. 1a–d) and 4 experimental complex structures from the Protein Data Bank (PDB, Fig. 2a–d). For these 4 experimental…

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How do you deal with proteins having large loop? – User discussions

GROMACS version: GROMACS 2023.3GROMACS modification: No I am preparing files for protein-ligand simulation for PPAR alpha. The protein structure available on PDB has two truncated loops. These truncated loops introduced the artifact of long bond distances during energy minimization. If I include the loop, the system will be very large,…

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How to get PDB file from lammpstrj files – LAMMPS General Discussion

Hi All, I have generated the LAMMPS data file using the CA atom coordinate of the PDB file, run the LAMMPS simulation, and got the lammpstrj file. now, I have the last snapshot of the trajectory file and try to generate the PDB file.Is it possible to get the PDB…

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RCSB PDB – 8EAE: Structure of Ternary Complex of cGAS with dsDNA and Bound 5-pppG(2,5)pI

VLO (Subject of Investigation/LOI)Query on VLO Download Ideal Coordinates CCD File&nbsp Download Instance Coordinates  G [auth A],J [auth C] [[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphateC20 H27 N9 O21 P4QIEFBLFMZQEZSF-INFSMZHSSA-N  Ligand Interaction Read more here: Source link

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Map genome positions onto protein coordinates?

I am looking for a way to do the following 1) reliably find a protein structure e.g. pdb file or pre-computed alphafold results that is associated with a particular gene/transcript isoform. I found a way to do this somewhat for human genes using biomart, but i’d like to be able…

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Need assistance in proper binding of cysteines

Need assistance in proper binding of cysteines 0 Hello! I am newbie in protein building and i need to create disulfide bond between newly builded cysteine and another one to form active site for my ligand. Further i need to dock small molecule in this site. Is there any tools…

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Transferring xyz coordinates between PDB files

Transferring xyz coordinates between PDB files 0 Hi, I have two pdb files (there are no PDB identifications). I wanna transfer xyz coordinates of specific residues from one pdb to another. How can I do this? Is there any tool for doing this? pdb • 43 views • link updated…

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Uses of Package org.biojava.bio.structure.jama (BioJava-1.7 API)

Packages that use org.biojava.bio.structure.jama org.biojava.bio.structure Interfaces and classes for protein structure (PDB).  org.biojava.bio.structure.align Classes for the super-imposition of structures.  org.biojava.bio.structure.align.helper Helper classes for structural alignment.  org.biojava.bio.structure.align.pairwise Classes for the pairwise alignment of structures.  org.biojava.bio.structure.gui A few convenience classes to view protein structures with Jmol (if it is on the classpath),…

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Computational Methods for Predicting ncRNA-protein Interactions

Title:Computational Methods for Predicting ncRNA-protein Interactions Volume: 13 Issue: 6 Author(s): Shao-Wu Zhang*Xiao-Nan Fan Affiliation: Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi’an, 710072,China Keywords: ncRNA-protein interaction, prediction, dataset construction, feature representation, machine learning, RNA purification. Abstract: Background: RNA-protein interactions (RPIs)…

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EMDB < EMD-25228

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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