Tag: pdb

RCSB PDB – 7SBA: Structure of type I-D Cascade bound to a dsDNA target

CRISPR-Cas systems are adaptive immune systems that protect prokaryotes from foreign nucleic acids, such as bacteriophages. Two of the most prevalent CRISPR-Cas systems include type I and type III. Interestingly, the type I-D interference proteins contain characteristic features of both type I and type III systems … CRISPR-Cas systems are…

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KEGG T01003: 286761

Entry 286761            CDS       T01003                                  Symbol Vcpip1 Name (RefSeq) deubiquitinating protein VCPIP1   KO K11861   deubiquitinating protein VCIP135 [EC:3.4.19.12] Organism rno  Rattus norvegicus (rat) Brite KEGG Orthology (KO) [BR:rno00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:rno01002]    286761 (Vcpip1)  09182 Protein families: genetic information processing   04121 Ubiquitin system [BR:rno04121]    286761 (Vcpip1)Enzymes [BR:rno01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.19  Omega peptidases    3.4.19.12  ubiquitinyl…

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[PyMOL] PyMol & PDBe

Hi Filip, This is already done. The update was in PyMOL 1.8.4.2 and in Open-Source PyMOL rev 4165. The object names are still the same, so it’s backwards compatible. The only difference is the file format, previously we downloaded omap format, now it’s ccp4 map format (larger files but higher…

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RCSB PDB – 7V94: Cryo-EM structure of the Cas12c2-sgRNA-target DNA ternary complex

RNA-guided CRISPR-Cas nucleases are widely used as versatile genome-engineering tools. Recent studies identified functionally divergent type V Cas12 family enzymes. Among them, Cas12c2 binds a CRISPR RNA (crRNA) and a trans-activating crRNA (tracrRNA) and recognizes double-stranded DNA targets with a short TN PAM … RNA-guided CRISPR-Cas nucleases are widely used…

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Cannot compile any CUDA program – CUDA Programming and Performance

I am getting the following error when I run sample programs on vs 2022.My details:Windows 11 x64GTX 1650i7 9gen8 gb ram Severity Code Description Project File Line Suppression State Error MSB3721 The command C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.6\bin\nvcc.exe -gencode=arch=compute_35,code=\sm_35,compute_35\ -gencode=arch=compute_37,code=\sm_37,compute_37\ -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\ –use-local-env -ccbin…

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Bioinformatician/Scientific Programmer job with EMBL

We seek to recruit a structural bioinformatician who is interested in working on the intersection of bioinformatics and cheminformatics. The post holder will join the Velankar team at EMBL-EBI on a 2-year collaborative project between PDBe, ChEMBL and CCDC. They will contribute to improving data processing pipelines to increase the…

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Double precision on gro file using editconf – User discussions

GROMACS version:2022.1GROMACS modification: NoIs there a way to keep the position coordinate in DP? The gro file seems to revert back to SP when it get converted from pdb to gro by editconf. I can rewrite them into DP but I do not know how to keep DP when the…

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Extensively drug resistant E. coli LZ00114

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

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A-Prot: protein structure modeling using MSA transformer | BMC Bioinformatics

Benchmarking contact prediction First, we benchmarked the long-range contact prediction performance of A-Prot using the FM and FM/TBM targets of CASP13 [24]. The benchmark results show that the performance of our model outperforms that of the existing methods (Table 1). We compared the precision of our model’s top L/5, L/2,…

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[BioPython] ModuleNotFoundError: No module named Bio.PDB.SASA

[BioPython] ModuleNotFoundError: No module named Bio.PDB.SASA 2 Hello, I am trying to calculate the solvent accessible surface of pdb files using Biopython. Specifically I am trying to deduce the interaction surface of complex by substracting the solvent accessible surface of both unbound structure to the solvent accessible surface of the…

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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

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biopython – Identify side chain atoms in BioPandas dataframe

As you suggest one way of solving your problem would be by selecting all atoms that don’t have backbone atoms names. In a pdb file I believe backbone atoms would be named ‘CA’, ‘HA’, ‘N’, ‘HN’ or ‘H’, ‘C’ and ‘O’. Beware of the N-terminal (where the hydrogens would be…

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Change of protein-protein-interaction free energy upon ligand binding (procedure and controls) – User discussions

GROMACS version: 2021.1GROMACS modification: No Dear Gromacs and simulation community, in the course of my master’s thesis, I want to determine the protein-protein-binding free energy between two GTPases using PMF calculations via umbrella sampling. Especially I am interested in the contribution of the bound nucleotides (one per protein) which are…

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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

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molecular dynamics – How to generate a .tpr file from a .pdb or .xyz file in gromacs

For generating a tpr file, you need a topology file (.top), a coordinate file (.gro/.pdb) and a input parameter file (.mdp). Assuming, you are working with amber forcefield (a99ffSBdisp), Here’s how I do it. gmx pdb2gmx -ff a99SBdisp -f yourpdbfile.pdb -o water_1.gro -ignh -p topol.top gmx grompp -f water.mdp -c…

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Maestro (schrodinger) data in PyMOL : comp_chem

Hello everyone, I recently ran some docking experiments in Maestro at a university computer. The problem is that I cannot be at that computer all the time. Is it possible to open the data in, for example, PyMOL so I can work on my personal computer? And if so, would…

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Bioinformatician job with EMBL | 1401746299

Are you creative, curious, and ambitious and like to tackle challenging biological data analysis problems? We have an exciting opportunity for a bioinformatician interested in structural biological data and functional annotations to work within the Protein Data Bank in Europe Team (PDBe) at the European Bioinformatics Institute (EMBL-EBI). In this…

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RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder

Significance Hairpin pyrrole-imidazole (Py-Im) polyamides can be programmed to bind a broad repertoire of DNA sequences. Py-Im small molecules can be used to target cancer-specific coding regions and block transcription elongation. This transcription blockage by Py-Im cannot be rescued by transcription elongation factors, such as TFIIS. The mechanism by which…

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Comprehensive, hands-on tutorial for DNA-ligand MDS – User discussions

GROMACS version: 2021.4-HomebrewGROMACS modification: No Hello, guys. I am very new to molecular dynamics and I come from biomedical background. Recently, my boss asked me to gather additional data about interaction of a small molecule and an aberrant double-stranded DNA structure. I originally did docking experiments in Vina, and he…

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computational chemistry – Troubleshooting an Autodock Vina Error on Chimera: “Could not find an atomic number for Hn Hn”

After having minimized a ligand (that I prepared on Marvinsketch), and after having prepared a target enzyme to dock said ligand onto (collected from RCSP PDB), I was met with an error by the reply log stating that it “could not find atomic number for Hn Hn”. As a new…

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Beauty at a molecular level

About PDBe > News > 2022 Calendar: Beauty at a molecular level 2022 Calendar: Beauty at a molecular level ‘Tis the season for the new PDBe calendar! Our calendar for 2022 is now available to view and print – just in time for the New Year. The PDBe calendar for 2022 is…

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Applications of AlphaFold beyond Protein Structure Prediction

Abstract Predicting structures accurately for natural protein sequences by DeepMind’s AlphaFold is certainly one of the greatest breakthroughs in biology in the twenty-first century. For designed or engineered sequences, which can be unstable, predicting the stabilities together with their structures is essential since unstable structures will not function properly. We…

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Representable, non-homologous, non-redundant protein database

Representable, non-homologous, non-redundant protein database 1 Hello, i’m examining properties of proteins secondary structures and for examining and presenting the results: What non-redundant (or non-homologous) protein database would you recommend? I’ve obtained a list of PDB ids from PISCES (dunbrack.fccc.edu/pisces/) and obtained the protein details from UniProt, however i’m not…

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How do I view data in pymol via Ipymol for visualisation in a Jupyter notebook?

Question: How do I view data in pymol via Ipymol for visualisation in a Jupyter notebook? 1 I am analysing protein data using Python programming language and Jupyter notebook. In the Terminal I have put an alias in a hidden file on the home directory entitled .bash_profile, in order to…

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How to download all structures of complexes in PDB

How to download all structures of complexes in PDB 1 Dear all, Does anyone know how to download all structures of complexes in PDB? For complex I mean the structures containing more than one chains which forms biological interactions with each other? Is there any search filter in pdb With…

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Postdoctoral Fellow job with Cleveland Clinic – Genomic Medicine Institute

We are seeking multiple Experimental and Bioinformatics research positions (including Postdoctoral Research Fellows and Research Associate) to join the Alzheimer’s Network Medicine and Artificial Intelligence (AI) research group (www.lerner.ccf.org/gmi/cheng/) led by Dr. Feixiong Cheng at the Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, and Department of Molecular Medicine at…

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Downloading filtered PDB files

Downloading filtered PDB files 1 I want to download 28000 fasta files from the PDB. I applied some filters on the resolution, length, etc of the proteins. However, I cannot directly download them from the website since it only allows a 2500-sequences batch download. How can I make this download…

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Epistasis shapes the fitness landscape of an allosteric specificity switch

Computational design Protein modeling and design was performed with Rosetta version 3.5 (2015.19.57819)35,37. Python and shell scripts for generating input from Rosetta and analyzing from Rosetta are available at: github.com/raman-lab/biosensor_design The high-resolution TtgR structure co-crystalized with tetracycline was selected as the starting point for computational design (PDB: 2UXH)28. The structure…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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Biopython Contact Map | Contact Information Finder

Listing Results Biopython Contact Map Protein Contact Maps using Biopython Warwick 9 hours ago Warwick.ac.uk View All Protein Contact Maps using Biopython. When working with protein 3D structures, a contact map is usually defined as a binary matrix with the rows and columns representing the residues of two different chains….

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protti source: R/fetch_alphafold_prediction.R

#’ Fetch AlphaFold prediction #’ #’ Fetches atom level data for AlphaFold predictions either for selected proteins or whole #’ organisms. #’ #’ @param uniprot_ids optional, a character vector of UniProt identifiers for which predictions #’ should be fetched. This argument is mutually exclusive to the code{organism_name} argument. #’ @param…

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Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Peptides are mapped onto PDB structures or AlphaFold prediction based on their positions. This is accomplished by replacing the B-factor information in the structure file with values that allow highlighting of peptides, protein regions or amino acids when the structure is coloured by B-factor. In addition to simply highlighting peptides,…

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Precomputed secondary structure prediction from sequence

Precomputed secondary structure prediction from sequence 2 Hi, Most services that predict secondary structure from sequence, such as psipred, have an online webserver or a program you’d have to run locally (which would take quite a bit for a whole proteome). e.g. bioinf.cs.ucl.ac.uk/psipred/result/0fc9a438-c3d8-11e3-a745-00163e110593 I was wondering if anyone knew a…

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Install alphafold on the local machine, get out of docker.

AlphaFold This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from…

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Open multi-file AlphaFold models | ChimeraX Recipes

# # Open AlphaFold database models for proteins larger than 1400 amino acids. # These calculated in 1400 amino acid segments every 200 amino acids due to # limitations (GPU memory) of the AlphaFold software. We load and align # the segment models. This produces many clashes. # # Opening…

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alphafold colab github

for the third time worked! Found inside – Page iiThe eight-volume set comprising LNCS volumes 9905-9912 constitutes the refereed proceedings of the 14th European Conference on Computer Vision, ECCV 2016, held in Amsterdam, The Netherlands, in October 2016. Please make sure you have a large enough hard drive space, bandwidth…

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BLASTP version 4 database error *Help

I am having trouble running the blastp command. When I run this command against the Swiss-prot database installed from the NCBI i get this error $ blastp -db swissprot -query Ecoli_rpoB.fasta -out TEST15.txt BLAST Database error: Error: Not a valid version 4 database. However, when I create my own database…

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rosetta fold vs alphafold 2

S. Both AlphaFold and Xu use simple folding engines L-BFGS (L- Broyden–Fletcher–Goldfarb– Shanno (BFGS)) and CNS (Crystallography and NMR System), respectively, i.e., improvements come from a better energy potential using distributional information. The phase problem is a problem, to the point that in the past decade, several structures, such as M-PMV…

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Pymolrc settings help in pymol

Pymolrc settings help in pymol 0 Hello, I wanted to set up pymol, so I get the highest resolution every time it starts. this can be done in the Pymolrc file. this file can be accessed via file->edit pymolrc my code for pymolrc is bg white util.performance(0) rebuild and I…

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SIte Mutations in a 3D protein structure to locate the core of mutations

SIte Mutations in a 3D protein structure to locate the core of mutations 0 Hello Everyone, I have a pdb file for a protein (3D structure predicted by a tool) and around hundreds of known point mutations in the protein. I want to visualize the protein with all the mutations…

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How I can merge 2 pdb files correctly on pyMol

How I can merge 2 pdb files correctly on pyMol 1 Hi there, Please, I’m not experienced in this field and I need help. I want to check the ligand-interaction of 2 molecules, but I’m not able to merge the 2 PDB files correctly, because it’s like the ligand is…

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Topology generation for non-standard molecules in GROMACS : comp_chem

I have just started working in the field of molecular dynamics and using gromacs for my studies. The problem that I am facing is topology generation for non-standard molecules. I looked into the gromacs manual on how to add residue to a forcefield but that is quite confusing. I started…

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What No One Is Talking About

In this next installment of our AlphaFold Series, we look at the potential drawbacks and limitations of the approach. There is no doubt that AlphaFold is a breakthrough in protein structure prediction, and we have commented on some of the exciting opportunities it presents. In mid-Aug 2021, two weeks after…

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How to download data for visualising and analysing in RINalyzer in Cytoscape.

How to download data for visualising and analysing in RINalyzer in Cytoscape. 1 I am new to this plugin in Cytoscape. I want to visualise RIN from pdb and analyze the network. According to the tutorial we can download daat from RIN data websever. But when I am trying to…

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Can i estimate the hormone-receptor binding affinity ?

Can i estimate the hormone-receptor binding affinity ? 0 Hello everyone! I dont know if anyone can help me but i want to know if i can estimate the hormone-receptor bindind affinity (Kd) using a software. The hormone is Estrone and the receptor is Estrogen receptor alpha. I have the…

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Has anybody used RIP-MD tool for generation of RIN from MD trajectories?

Has anybody used RIP-MD tool for generation of RIN from MD trajectories? 0 I have been trying to use the RIP-MD tool for generating residue interaction networks from pdb file and MD trajectories. I have tried installing the VMD plugin and running the files through that for the same. But…

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AutoDock Flexible Molecular Docking Tutorial

AutoDock Flexible Molecular Docking Tutorial Autodock is a molecular docking software package, open source and free, the official website is autodock.scripps.edu/, the latest version is AutoDock 4.2.6, including AutoDock and AutoGrid two modules, AutoDock software package download address It is autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/, including Linux, Mac OS and Windows versions…

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Ligand GNP bound in PDB entry 7obq ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

  The above 2D and 3D (Mol*) views of ligand interactions use quaternary structure derived from the PDB entry. Please note: Some chain IDs in the tooltip are followed by a number in square brackets. This number corresponds to the operation ID (mmCIF ‘oper_expression’) used to transform the chain. The…

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Extracting coordinates of possibly H bonded solvent molecule using BioPython

Extracting coordinates of possibly H bonded solvent molecule using BioPython 0 Hi, I am trying to extract the coordinates of solvent molecule from a peptide PDB, within a distance of 3 ang of O and N atoms in peptide. Using VMD, I can extract up to 3 ang of peptide….

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split pdb into submodels

split pdb into submodels 1 There is a program called pdbsplitchains in this repository: github.com/ACRMGroup/bioptools pdbset from the CCP4 package can do all kinds of manipulations on PDB files – including splitting by chain – but it requires a bit of scripting. For example, these several lines would extract chain…

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Alternative way to generate .PDBQT file for AutoDock Vina? : bioinformatics

For context: I’m using macOS Big Sur and have successfully run AutoDock Vina through my terminal, after which I’ll view the output in ChimeraX. Also, I’m an undergrad attempting to teach myself how to use docking software for a personal project and future use, so I may very well have…

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The LpoA activator is required to stimulate the peptidoglycan polymerase activity of its cognate cell wall synthase PBP1a

Significance Class A penicillin-binding proteins (aPBPs) assemble the bacterial cell wall and are the targets of penicillin and related β-lactam antibiotics. In gram-negative bacteria, the aPBPs require outer membrane lipoproteins to function. However, little is known about how these proteins promote the activity of their cognate synthases in cells. Here,…

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Search PDB-format files for residue contacts

Search PDB-format files for residue contacts 1 I am looking for a program that can process a large number of protein stuctures (PDB-format) and search the coordinates for a given criterion, or better, a combination of such criteria. A possible query would be: “return all instances where a lysine epsilon…

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Interface residue

Interface residue 0 I have a csv file of pdb ids and the interacting chains. i want to find the interface residues within 5A cuttoff. Can someone help with the python code. Reaally urgent. find how using python the to interface residues • 26 views Login before adding your answer….

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Banking on protein structural data

PHOTO: WENDIE BERG In 1953, the proposed structure of DNA magnificently linked biological function and structure. By contrast, 4 years later, the first elucidation of the structure of a protein—myoglobin, by Kendrew and colleagues—revealed an inelegant shape, described disdainfully as a “visceral knot.” Additional complexity, as well as some general…

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Is there a way to separate the chains belong to each Biological assembly in a PDB file?

Is there a way to separate the chains belong to each Biological assembly in a PDB file? 1 I want to separate the chain IDs which belong to specific Biological assemblies in a PDB file. As an Example PDB ID 1BRS has 3 Biological assemblies Biological assembly 1 : –…

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New Mac program for molecular biologists

Tool:New Mac program for molecular biologists 12 I would like to present here a program – BioLabDonkey – for molecular biologists who are Mac users. This program is written from scratch in a language native for Mac – Swift. The program can be downloaded from mac App Store – apps.apple.com/us/app/biolabdonkey/id1470827582?ls=1&mt=12…

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Sequence (annotation) databases in 2021

Forum:Sequence (annotation) databases in 2021 1 Hi everyone, So I know there are several threads on this topic already (or tangentially related to it). For example: But these threads are really old now. Things have probably changed quite significantly in the mean time. So I would like to start a…

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how to find interference residue

how to find interference residue 1 Are you asking about interacting residue in protein-protein interfaces? If so, this server takes a PDB file and will calculate the interface residues. www.ebi.ac.uk/pdbe/pisa/ Login before adding your answer. Traffic: 1660 users visited in the last hour Read more here: Source link

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Answer: alphafold online availability and use case

1. There is no need for heavy-duty methods such as AlphaFold2 (AF2) in all cases. It is very unlikely that you have 1500 sequences that only have domains of unknown function, and even if you do, there were successful structure prediction servers in existence before AF2. So even though what…

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how to calculate positive and negative for a given protein sequence

how to calculate positive and negative for a given protein sequence 0 Hello, I would like to know how once could calculate positive and negative for a given sequence? The PDB of the protein is 1ak4. It has two chain A and B. I am looking to find a way…

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Output Polar Contacts Between Chains to Text File

  PYMOL: Output Polar Contacts Between Chains to Text File 0   I am new to PyMOL but have a very specific task that I need to do. I have a PDB structure file of protein homo-oligomer, and I want to use PyMol to determine polar contacts between chain A…

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How To Perform Peptide-Protein Docking

How To Perform Peptide-Protein Docking 4 Hi, could anybody give me an example about how to perform peptide-protein docking: the software and steps?Here is my problem:(1) a peptide about 10 amino acids(2) target protein (an enzyme with known PDB structure file, and known active sites)(3) how to find the most…

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How can I get the exact 3D structure of the protein to use the PDB file for PPI docking

How can I get the exact 3D structure of the protein to use the PDB file for PPI docking 1 I am working on an uncharacterized protein, and I need to know its PPI with rna polymrase in humans. Please, how can I get the exact 3D structure of the…

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PyMol – molecule export problem

PyMol – molecule export problem 0 Dear all, I have a molecule in PyMol which I want to open in ChimeraX. But after exporting the molecule as .pdb, some structural information seems to be lost – regions that in the PyMol session file are embedded into helices are now loops…

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