Protein Science

article

New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics

Michael G. Prisant, Christopher J. Williams, Vincent B. Chen, Jane S. Richardson, more

The MolProbity web service provides macromolecular model validation to help correct local errors, for the structural biology community worldwide. Here we highlight new validation features, and also describe how we are fighting back against outside developments which compromise that mission. Our new tool called UnDowser analyzes the properties and context of clashing HOH “waters” to diagnose what they...

article

Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

Joseph Laureanti, Juan Brandi, Elvis Offor, David Engel, more

Protein Science > 29 > 1 > 237 - 246

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the...

article

Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation

Alexander S. Ford, Brian D. Weitzner, Christopher D. Bahl

Protein Science > 29 > 1 > 43 - 51

The Rosetta software suite for macromolecular modeling is a powerful computational toolbox for protein design, structure prediction, and protein structure analysis. The development of novel Rosetta‐based scientific tools requires two orthogonal skill sets: deep domain‐specific expertise in protein biochemistry and technical expertise in development, deployment, and analysis of molecular simulations...

article

Collection of antimicrobial peptides database and its derivatives: Applications and beyond

Faiza Hanif Waghu, Susan Idicula‐Thomas

Protein Science > 29 > 1 > 36 - 42

Collection of antimicrobial peptides (CAMP), CAMPSign, and ClassAMP are open‐access resources that have been developed to enhance research on antimicrobial peptides (AMPs). Comprehensive information on AMPs and machine learning‐based predictive models are made available for users through these resources. As of date, CAMP_R3 has 10,247 sequences, 757 structures, and 114 family‐specific signatures of...

article

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

David S. Goodsell, Christine Zardecki, Luigi Di Costanzo, Jose M. Duarte, more

Protein Science > 29 > 1 > 52 - 65

Analyses of publicly available structural data reveal interesting insights into the impact of the three‐dimensional (3D) structures of protein targets important for discovery of new drugs (e.g., G‐protein‐coupled receptors, voltage‐gated ion channels, ligand‐gated ion channels, transporters, and E3 ubiquitin ligases). The Protein Data Bank (PDB) archive currently holds > 155,000 atomic‐level 3D...

article

Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations

Ji Young Lee, James M. Krieger, Hongchun Li, Ivet Bahar

Protein Science > 29 > 1 > 76 - 86

Recent years have seen progress in druggability simulations, that is, molecular dynamics simulations of target proteins in solutions containing drug‐like probe molecules to characterize their drug‐binding abilities, if any. An important consecutive step is to analyze the trajectories to construct pharmacophore models (PMs) to use for virtual screening of libraries of small molecules. While considerable...

article

SASBDB: Towards an automatically curated and validated repository for biological scattering data

Alexey G. Kikhney, Clemente R. Borges, Dmitry S. Molodenskiy, Cy M. Jeffries, more

Protein Science > 29 > 1 > 66 - 75

Small‐angle scattering (SAS) of X‐rays and neutrons is a fundamental tool to study the nanostructural properties, and in particular, biological macromolecules in solution. In structural biology, SAS recently transformed from a specialization into a general technique leading to a dramatic increase in the number of publications reporting structural models. The growing amount of data recorded and published...

article

Cryo‐EM map interpretation and protein model‐building using iterative map segmentation

Thomas C. Terwilliger, Paul D. Adams, Pavel V. Afonine, Oleg V. Sobolev

Protein Science > 29 > 1 > 87 - 99

A procedure for building protein chains into maps produced by single‐particle electron cryo‐microscopy (cryo‐EM) is described. The procedure is similar to the way an experienced structural biologist might analyze a map, focusing first on secondary structure elements such as helices and sheets, then varying the contour level to identify connections between these elements. Since the high density in...

article

SimpleDSFviewer: A tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions

Changye Sun, Yong Li, Edwin A. Yates, David G. Fernig

Protein Science > 29 > 1 > 19 - 27

Differential scanning fluorimetry (DSF) is a widely used thermal shift assay for measuring protein stability and protein–ligand interactions that are simple, cheap, and amenable to high throughput. However, data analysis remains a challenge, requiring improved methods. Here, the program SimpleDSFviewer, a user‐friendly interface, is described to help the researchers who apply DSF technique in their...

article

The antimicrobial peptide database provides a platform for decoding the design principles of naturally occurring antimicrobial peptides

Guangshun Wang

Protein Science > 29 > 1 > 8 - 18

This article is written for the 2020 tool issue of Protein Science. It briefly introduces the widely used antimicrobial peptide database, initially online in 2003. After a description of the main features of each database version and some recent additions, the focus is on the peptide design parameters for each of the four unified classes of natural antimicrobial peptides (AMPs). The amino acid signature...

article

A three‐dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor‐NIH protein structure determination

Charles D. Schwieters, Guillermo A. Bermejo, G. Marius Clore

Protein Science > 29 > 1 > 100 - 110

We introduce a new hydrogen bonding potential of mean force generated from high‐quality crystal structures for use in Xplor‐NIH structure calculations. This term applies to hydrogen bonds involving both backbone and sidechain atoms. When used in structure refinement calculations of 10 example protein systems with experimental distance, dihedral and residual dipolar coupling restraints, we demonstrate...

article

KEGG Mapper for inferring cellular functions from protein sequences

Minoru Kanehisa, Yoko Sato

Protein Science > 29 > 1 > 28 - 35

KEGG is a reference knowledge base for biological interpretation of large‐scale molecular datasets, such as genome and metagenome sequences. It accumulates experimental knowledge about high‐level functions of the cell and the organism represented in terms of KEGG molecular networks, including KEGG pathway maps, BRITE hierarchies, and KEGG modules. By the process called KEGG mapping, a set of protein...

article

Peppy: A virtual reality environment for exploring the principles of polypeptide structure

David G. Doak, Gareth S. Denyer, Juliet A. Gerrard, Joel P. Mackay, more

Protein Science > 29 > 1 > 157 - 168

A key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two‐dimensional (2D) images on paper, physical molecular modeling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic 3D nature of proteins. We have built a virtual reality...

article

NAGbinder: An approach for identifying N‐acetylglucosamine interacting residues of a protein from its primary sequence

Sumeet Patiyal, Piyush Agrawal, Vinod Kumar, Anjali Dhall, more

Protein Science > 29 > 1 > 201 - 210

N‐acetylglucosamine (NAG) belongs to the eight essential saccharides that are required to maintain the optimal health and precise functioning of systems ranging from bacteria to human. In the present study, we have developed a method, NAGbinder, which predicts the NAG‐interacting residues in a protein from its primary sequence information. We extracted 231 NAG‐interacting nonredundant protein chains...

article

Molstack: A platform for interactive presentations of electron density and cryo‐EM maps and their interpretations

Przemyslaw J. Porebski, Grzegorz Bokota, Barat S. Venkataramany, Wladek Minor

Protein Science > 29 > 1 > 120 - 127

In the Special Issue on Tools for Protein Science in 2018, we presented Molstack: a concept of a cloud‐based platform for sharing electron density maps and their interpretations. Molstack is a web platform that allows the interactive visualization of density maps through the simultaneous presentation of multiple datasets and models in a way that allows for easy pairwise comparison. We anticipated...

article

VarSite: Disease variants and protein structure

Roman A. Laskowski, James D. Stephenson, Ian Sillitoe, Christine A. Orengo, more

Protein Science > 29 > 1 > 111 - 119

VarSite is a web server mapping known disease‐associated variants from UniProt and ClinVar, together with natural variants from gnomAD, onto protein 3D structures in the Protein Data Bank. The analyses are primarily image‐based and provide both an overview for each human protein, as well as a report for any specific variant of interest. The information can be useful in assessing whether a given variant...

article

Hybrid Electron Microscopy Normal Mode Analysis with Scipion

Mohamad Harastani, Carlos Oscar S. Sorzano, Slavica Jonić

Protein Science > 29 > 1 > 223 - 236

Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) method was introduced in 2014. HEMNMA computes normal modes of a reference model (an atomic structure or an electron microscopy map) of a molecular complex and uses this model and its normal modes to analyze single‐particle images of the complex to obtain information on its continuous conformational changes, by determining the full distribution...

article

Flexible docking of peptides to proteins using CABS‐dock

Mateusz Kurcinski, Aleksandra Badaczewska‐Dawid, Michal Kolinski, Andrzej Kolinski, more

Protein Science > 29 > 1 > 211 - 222

Molecular docking of peptides to proteins can be a useful tool in the exploration of the possible peptide binding sites and poses. CABS‐dock is a method for protein–peptide docking that features significant conformational flexibility of both the peptide and the protein molecules during the peptide search for a binding site. The CABS‐dock has been made available as a web server and a standalone package...

article

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions—Insights from transcription factors

Peter S. Millard, Katrine Bugge, Riccardo Marabini, Wouter Boomsma, more

Protein Science > 29 > 1 > 169 - 183

Protein domains constitute regions of distinct structural properties and molecular functions that are retained when removed from the rest of the protein. However, due to the lack of tertiary structure, the identification of domains has been largely neglected for long (>50 residues) intrinsically disordered regions. Here we present a sequence‐based approach to assess and visualize domain organization...

article

DALI and the persistence of protein shape

Liisa Holm

Protein Science > 29 > 1 > 128 - 140

DALI is a popular resource for comparing protein structures. The software is based on distance‐matrix alignment. The associated web server provides tools to navigate, integrate and organize some data pushed out by genomics and structural genomics. The server has been running continuously for the past 25 years. Structural biologists routinely use DALI to compare a new structure against previously known...

INFONA - science communication portal

Protein Science

New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics

Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation

Collection of antimicrobial peptides database and its derivatives: Applications and beyond

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations

SASBDB: Towards an automatically curated and validated repository for biological scattering data

Cryo‐EM map interpretation and protein model‐building using iterative map segmentation

SimpleDSFviewer: A tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions

The antimicrobial peptide database provides a platform for decoding the design principles of naturally occurring antimicrobial peptides

A three‐dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor‐NIH protein structure determination

KEGG Mapper for inferring cellular functions from protein sequences

Peppy: A virtual reality environment for exploring the principles of polypeptide structure

NAGbinder: An approach for identifying N‐acetylglucosamine interacting residues of a protein from its primary sequence

Molstack: A platform for interactive presentations of electron density and cryo‐EM maps and their interpretations

VarSite: Disease variants and protein structure

Hybrid Electron Microscopy Normal Mode Analysis with Scipion

Flexible docking of peptides to proteins using CABS‐dock

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions—Insights from transcription factors

DALI and the persistence of protein shape

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