Search Results - "Protein science"

UCSF ChimeraX: Structure visualization for researchers, educators, and developers by Pettersen, Eric F., Goddard, Thomas D., Huang, Conrad C., Meng, Elaine C., Couch, Gregory S., Croll, Tristan I., Morris, John H., Ferrin, Thomas E.

“…UCSF ChimeraX is the next‐generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following…”
Get full text

UCSF ChimeraX: Tools for structure building and analysis by Meng, Elaine C., Goddard, Thomas D., Pettersen, Eric F., Couch, Greg S., Pearson, Zach J., Morris, John H., Ferrin, Thomas E.

“…Advances in computational tools for atomic model building are leading to accurate models of large molecular assemblies seen in electron microscopy, often at…”
Get full text

Toward understanding the origin and evolution of cellular organisms by Kanehisa, Minoru

“…In this era of high‐throughput biology, bioinformatics has become a major discipline for making sense out of large‐scale datasets. Bioinformatics is usually…”
Get full text

PANTHER: Making genome‐scale phylogenetics accessible to all by Thomas, Paul D., Ebert, Dustin, Muruganujan, Anushya, Mushayahama, Tremayne, Albou, Laurent‐Philippe, Mi, Huaiyu

“…Phylogenetics is a powerful tool for analyzing protein sequences, by inferring their evolutionary relationships to other proteins. However, phylogenetics…”
Get full text

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions by Oughtred, Rose, Rust, Jennifer, Chang, Christie, Breitkreutz, Bobby‐Joe, Stark, Chris, Willems, Andrew, Boucher, Lorrie, Leung, Genie, Kolas, Nadine, Zhang, Frederick, Dolma, Sonam, Coulombe‐Huntington, Jasmin, Chatr‐aryamontri, Andrew, Dolinski, Kara, Tyers, Mike

“…The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open‐access database resource that houses manually curated protein…”
Get full text

KEGG mapping tools for uncovering hidden features in biological data by Kanehisa, Minoru, Sato, Yoko, Kawashima, Masayuki

“…In contrast to artificial intelligence and machine learning approaches, KEGG (https://www.kegg.jp) has relied on human intelligence to develop “models” of…”
Get full text

KEGG Mapper for inferring cellular functions from protein sequences by Kanehisa, Minoru, Sato, Yoko

“…KEGG is a reference knowledge base for biological interpretation of large‐scale molecular datasets, such as genome and metagenome sequences. It accumulates…”
Get full text

UCSF ChimeraX: Meeting modern challenges in visualization and analysis by Goddard, Thomas D., Huang, Conrad C., Meng, Elaine C., Pettersen, Eric F., Couch, Gregory S., Morris, John H., Ferrin, Thomas E.

“…UCSF ChimeraX is next‐generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It…”
Get full text

MolProbity: More and better reference data for improved all‐atom structure validation by Williams, Christopher J., Headd, Jeffrey J., Moriarty, Nigel W., Prisant, Michael G., Videau, Lizbeth L., Deis, Lindsay N., Verma, Vishal, Keedy, Daniel A., Hintze, Bradley J., Chen, Vincent B., Jain, Swati, Lewis, Steven M., Arendall, W. Bryan, Snoeyink, Jack, Adams, Paul D., Lovell, Simon C., Richardson, Jane S., Richardson, David C.

“…This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and…”
Get full text

Improvements to the APBS biomolecular solvation software suite by Jurrus, Elizabeth, Engel, Dave, Star, Keith, Monson, Kyle, Brandi, Juan, Felberg, Lisa E., Brookes, David H., Wilson, Leighton, Chen, Jiahui, Liles, Karina, Chun, Minju, Li, Peter, Gohara, David W., Dolinsky, Todd, Konecny, Robert, Koes, David R., Nielsen, Jens Erik, Head‐Gordon, Teresa, Geng, Weihua, Krasny, Robert, Wei, Guo‐Wei, Holst, Michael J., McCammon, J. Andrew, Baker, Nathan A.

“…The Adaptive Poisson–Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that…”
Get full text

Clustal Omega for making accurate alignments of many protein sequences by Sievers, Fabian, Higgins, Desmond G.

“…Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some…”
Get full text

DALI and the persistence of protein shape by Holm, Liisa

“…DALI is a popular resource for comparing protein structures. The software is based on distance‐matrix alignment. The associated web server provides tools to…”
Get full text

DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data by Miles, Andrew J., Ramalli, Sergio G., Wallace, B. A.

“…Circular dichroism (CD) spectroscopy is a widely‐used method for characterizing the secondary structures of proteins. The well‐established and highly used…”
Get full text

Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data by Casañal, Ana, Lohkamp, Bernhard, Emsley, Paul

“…Coot is a tool widely used for model building, refinement, and validation of macromolecular structures. It has been extensively used for crystallography and,…”
Get full text

PDBsum: Structural summaries of PDB entries by Laskowski, Roman A., Jabłońska, Jagoda, Pravda, Lukáš, Vařeková, Radka Svobodová, Thornton, Janet M.

“…PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image‐based and include…”
Get full text

The molecular details of cytokine signaling via the JAK/STAT pathway by Morris, Rhiannon, Kershaw, Nadia J., Babon, Jeffrey J.

“…More than 50 cytokines signal via the JAK/STAT pathway to orchestrate hematopoiesis, induce inflammation and control the immune response. Cytokines are…”
Get full text

Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV‐2 by Kim, Youngchang, Jedrzejczak, Robert, Maltseva, Natalia I., Wilamowski, Mateusz, Endres, Michael, Godzik, Adam, Michalska, Karolina, Joachimiak, Andrzej

“…Severe Acute Respiratory Syndrome coronavirus 2 (SARS‐CoV‐2) is rapidly spreading around the world. There is no existing vaccine or proven drug to prevent…”
Get full text

The human protein atlas: A spatial map of the human proteome by Thul, Peter J., Lindskog, Cecilia

“…The correct spatial distribution of proteins is vital for their function and often mis‐localization or ectopic expression leads to diseases. For more than a…”
Get full text

DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations by Rodrigues, Carlos H.M., Pires, Douglas E.V., Ascher, David B.

“…Predicting the effect of missense variations on protein stability and dynamics is important for understanding their role in diseases, and the link between…”
Get full text

DALI shines a light on remote homologs: One hundred discoveries by Holm, Liisa, Laiho, Aleksi, Törönen, Petri, Salgado, Marco

“…Structural comparison reveals remote homology that often fails to be detected by sequence comparison. The DALI web server…”
Get full text