Works matching DE "STRUCTURAL bioinformatics"

Results: 467

Unsupervised learning reveals landscape of local structural motifs across protein classes Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 7, p. 1, doi. 10.1093/bioinformatics/btaf377

By:

Derry, Alexander;
Krupkin, Haim;
Tartici, Alp;
Altman, Russ B

Publication type:

Article

On the Regularities of the Polar Profiles of Proteins Related to Ebola Virus Infection and their Functional Domains.

Published in:

Cell Biochemistry & Biophysics, 2018, v. 76, n. 3, p. 411, doi. 10.1007/s12013-018-0839-4

By:

Polanco, Carlos;
Samaniego Mendoza, José Lino;
Buhse, Thomas;
Uversky, Vladimir N.;
Bañuelos Chao, Ingrid Paola;
Bañuelos Cedano, Marcela Angola;
Tavera, Fernando Michel;
Tavera, Daniel Michel;
Falconi, Manuel;
Ponce de León, Abelardo Vela

Publication type:

Article

Definition of a New Information-Based Per-Residue Quality Parameter.

Published in:

Journal of Biomolecular NMR, 2005, v. 33, n. 2, p. 123, doi. 10.1007/s10858-005-2826-5

By:

Nabuurs, Sander B.;
Krieger, Elmar;
Spronk, Chris A. .E. M.;
Nederveen, Aart J.;
Vriend, Gert;
Vuister, Geerten W.

Publication type:

Article

Reweighted atomic densities to represent ensembles of NMR structures<sup>*</sup>.

Published in:

Journal of Biomolecular NMR, 2002, v. 23, n. 3, p. 221, doi. 10.1023/A:1019875223132

By:

Schwieters, Charles D.;
Clore, G. Marius

Publication type:

Article

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex.

Published in:

Molecules, 2022, v. 27, n. 3, p. 799, doi. 10.3390/molecules27030799

By:

Kumawat, Nitesh;
Tucs, Andrejs;
Bera, Soumen;
Chuev, Gennady N.;
Valiev, Marat;
Fedotova, Marina V.;
Kruchinin, Sergey E.;
Tsuda, Koji;
Sljoka, Adnan;
Chakraborty, Amit

Publication type:

Article

Structure-Dependent Activity of Plant-Derived Sweeteners.

Published in:

Molecules, 2020, v. 25, n. 8, p. 1946, doi. 10.3390/molecules25081946

By:

Ҫiçek, Serhat Sezai;
Sippl, Wolfgang;
Ntie-Kang, Fidele

Publication type:

Article

Human Copper-Containing Amine Oxidases in Drug Design and Development.

Published in:

Molecules, 2020, v. 25, n. 6, p. 1293, doi. 10.3390/molecules25061293

By:

Vakal, Serhii;
Jalkanen, Sirpa;
Dahlström, Käthe M.;
Salminen, Tiina A.;
Liu, Aimin

Publication type:

Article

Editorial of Special Issue Ruthenium Complex: The Expanding Chemistry of the Ruthenium Complexes.

Published in:

Molecules, 2015, v. 20, n. 9, p. 17244, doi. 10.3390/molecules200917244

By:

Dragutan, Ileana;
Dragutan, Valerian;
Demonceau, Albert

Publication type:

Article

A bibliometric study of bioinformatics research in South Africa.

Published in:

Scientometrics, 2009, v. 81, n. 1, p. 47, doi. 10.1007/s11192-007-2048-6

By:

Mohohlo Molatudi;
Neo Molotja;
Anastassios Pouris

Publication type:

Article

Molecular and crystal structure of trans and cis isomers of 3-cyano-4-[2-(4-methoxyphenyl)vinyl]-6,6-dimethyl-5,6-dihydro-2H-pyran.

Published in:

Chemistry of Heterocyclic Compounds, 2009, v. 45, n. 4, p. 417, doi. 10.1007/s10593-009-0279-6

By:

Belyakov, S.;
Fleisher, M.;
Jansone, D.;
Leite, L.;
Lukevics, E.

Publication type:

Article

Addition of Nitrile Oxides to N-Allylsaccharin.

Published in:

Chemistry of Heterocyclic Compounds, 2005, v. 41, n. 3, p. 393, doi. 10.1007/s10593-005-0160-1

By:

Dirnens, V.;
Belyakov, S.;
Lukevics, E.

Publication type:

Article

RNAloops: a database of RNA multiloops.

Published in:

Bioinformatics, 2022, v. 38, n. 17, p. 4200, doi. 10.1093/bioinformatics/btac484

By:

Wiedemann, Jakub;
Kaczor, Jacek;
Milostan, Maciej;
Zok, Tomasz;
Blazewicz, Jacek;
Szachniuk, Marta;
Antczak, Maciej

Publication type:

Article

Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4375, doi. 10.1093/bioinformatics/btab511

By:

Machat, Mohamed;
Langenfeld, Florent;
Craciun, Daniela;
Sirugue, Léa;
Labib, Taoufik;
Lagarde, Nathalie;
Maria, Maxime;
Montes, Matthieu

Publication type:

Article

BioCommons: a robust java library for RNA structural bioinformatics.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2766, doi. 10.1093/bioinformatics/btab069

By:

Zok, Tomasz

Publication type:

Article

Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations.

Published in:

Bioinformatics, 2021, v. 37, n. 10, p. 1367, doi. 10.1093/bioinformatics/btaa972

By:

Tripathi, Swarnendu;
Dsouza, Nikita R;
Urrutia, Raul;
Zimmermann, Michael T

Publication type:

Article

PyMod 3: a complete suite for structural bioinformatics in PyMOL.

Published in:

Bioinformatics, 2021, v. 37, n. 10, p. 1471, doi. 10.1093/bioinformatics/btaa849

By:

Janson, Giacomo;
Paiardini, Alessandro

Publication type:

Article

BioStructures.jl: read, write and manipulate macromolecular structures in Julia.

Published in:

Bioinformatics, 2020, v. 36, n. 14, p. 4206, doi. 10.1093/bioinformatics/btaa502

By:

Greener, Joe G;
Selvaraj, Joel;
Ward, Ben J

Publication type:

Article

DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins.

Published in:

Bioinformatics, 2020, v. 36, n. 7, p. 2105, doi. 10.1093/bioinformatics/btz863

By:

Zhang, Chengxin;
Zheng, Wei;
Mortuza, S M;
Li, Yang;
Zhang, Yang

Publication type:

Article

Lemon: a framework for rapidly mining structural information from the Protein Data Bank.

Published in:

Bioinformatics, 2019, v. 35, n. 20, p. 4165, doi. 10.1093/bioinformatics/btz178

By:

Fine, Jonathan;
Chopra, Gaurav

Publication type:

Article

Protein model quality assessment using 3D oriented convolutional neural networks.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3313, doi. 10.1093/bioinformatics/btz122

By:

Pagès, Guillaume;
Charmettant, Benoit;
Grudinin, Sergei

Publication type:

Article

Smooth orientation-dependent scoring function for coarse-grained protein quality assessment.

Published in:

Bioinformatics, 2019, v. 35, n. 16, p. 2801, doi. 10.1093/bioinformatics/bty1037

By:

Karasikov, Mikhail;
Pagès, Guillaume;
Grudinin, Sergei

Publication type:

Article

PySFD: comprehensive molecular insights from significant feature differences detected among many simulated ensembles.

Published in:

Bioinformatics, 2019, v. 35, n. 9, p. 1588, doi. 10.1093/bioinformatics/bty818

By:

Stolzenberg, Sebastian

Publication type:

Article

A natural upper bound to the accuracy of predicting protein stability changes upon mutations.

Published in:

Bioinformatics, 2019, v. 35, n. 9, p. 1513, doi. 10.1093/bioinformatics/bty880

By:

Montanucci, Ludovica;
Fariselli, Piero;
Martelli, Pier Luigi;
Ben-Tal, Nir

Publication type:

Article

Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODIGY-LIG web server.

Published in:

Bioinformatics, 2019, v. 35, n. 9, p. 1585, doi. 10.1093/bioinformatics/bty816

By:

Vangone, Anna;
Schaarschmidt, Joerg;
Koukos, Panagiotis;
Geng, Cunliang;
Citro, Nevia;
Trellet, Mikael E;
Xue, Li C;
Bonvin, Alexandre M J J

Publication type:

Article

High precision protein functional site detection using 3D convolutional neural networks.

Published in:

Bioinformatics, 2019, v. 35, n. 9, p. 1503, doi. 10.1093/bioinformatics/bty813

By:

Torng, Wen;
Altman, Russ B

Publication type:

Article

AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains.

Published in:

Bioinformatics, 2019, v. 35, n. 9, p. 1591, doi. 10.1093/bioinformatics/bty822

By:

Lapidoth, Gideon;
Fleishman, Sarel J;
Parker, Jake;
Prilusky, Jaime

Publication type:

Article

SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation.

Published in:

Bioinformatics, 2019, v. 35, n. 3, p. 462, doi. 10.1093/bioinformatics/bty635

By:

Jankauskaitė, Justina;
Dapkūnas, Justas;
Jiménez-García, Brian;
Fernández-Recio, Juan;
Moal, Iain H

Publication type:

Article

3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations.

Published in:

Bioinformatics, 2018, v. 34, n. 17, p. 3004, doi. 10.1093/bioinformatics/bty200

By:

Andronov, Leonid;
Michalon, Jonathan;
Ouararhni, Khalid;
Orlov, Igor;
Hamiche, Ali;
Vonesch, Jean-Luc;
Klaholz, Bruno P

Publication type:

Article

eMolTox: prediction of molecular toxicity with confidence.

Published in:

Bioinformatics, 2018, v. 34, n. 14, p. 2508, doi. 10.1093/bioinformatics/bty135

By:

Ji, Changge;
Svensson, Fredrik;
Zoufir, Azedine;
Bender, Andreas

Publication type:

Article

NGLview-interactive molecular graphics for Jupyter notebooks.

Published in:

Bioinformatics, 2018, v. 34, n. 7, p. 1241, doi. 10.1093/bioinformatics/btx789

By:

Nguyen, Hai;
Case, David A;
Rose, Alexander S

Publication type:

Article

Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 122, doi. 10.1093/bioinformatics/btx592

By:

Piovesan, Damiano;
Tosatto, Silvio C E

Publication type:

Article

NavMol 3.0: enabling the representation of metabolic reactions by blind users.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 120, doi. 10.1093/bioinformatics/btx556

By:

Binev, Yuri;
Peixoto, Daniela;
Pereira, Florbela;
Rodrigues, Ian;
Cavaco, Sofia;
Lobo, Ana M;
Aires-de-Sousa, João

Publication type:

Article

LightDock: a new multi-scale approach to protein--protein docking.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 49, doi. 10.1093/bioinformatics/btx555

By:

Jiménez-García, Brian;
Roel-Touris, Jorge;
Romero-Durana, Miguel;
Vidal, Miquel;
Jiménez-González, Daniel;
Fernández-Recio, Juan

Publication type:

Article

In silico structural modeling of multiple epigenetic marks on DNA.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 41, doi. 10.1093/bioinformatics/btx516

By:

Krawczyk, Konrad;
Demharter, Samuel;
Knapp, Bernhard;
Deane, Charlotte M;
Minary, Peter

Publication type:

Article

Cpipe: a comprehensive computational platform for sequence and structure-based analyses of Cysteine residues.

Published in:

Bioinformatics, 2017, v. 33, n. 15, p. 2395, doi. 10.1093/bioinformatics/btx181

By:

Soylu, Inanc;
Marino, Stefano M.

Publication type:

Article

Correlated mutations select misfolded from properly folded proteins.

Published in:

Bioinformatics, 2017, v. 33, n. 10, p. 1497, doi. 10.1093/bioinformatics/btx013

By:

Wozniak, P. P.;
Vriend, G.;
Kotulska, M.

Publication type:

Article

MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins.

Published in:

Bioinformatics, 2017, v. 33, n. 9, p. 1402, doi. 10.1093/bioinformatics/btx015

By:

Necci, Marco;
Piovesan, Damiano;
Dosztányi, Zsuzsanna;
Tosatto, Silvio C. E.

Publication type:

Article

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

Published in:

Bioinformatics, 2017, v. 33, n. 9, p. 1346, doi. 10.1093/bioinformatics/btw823

By:

Marks, Claire;
Nowak, Jaroslaw;
Klostermann, Stefan;
Georges, Guy;
Dunbar, James;
Jiye Shi;
Kelm, Sebastian;
Deane, Charlotte M.

Publication type:

Article

Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity.

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 1014, doi. 10.1093/bioinformatics/btw767

By:

Negi, Surendra S.;
Braun, Werner

Publication type:

Article

The structural bioinformatics library: modeling in biomolecular science and beyond.

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 997, doi. 10.1093/bioinformatics/btw752

By:

Cazals, Frédéric;
Dreyfus, Tom

Publication type:

Article

MIToS.jl: mutual information tools for protein sequence analysis in the Julia language.

Published in:

Bioinformatics, 2017, v. 33, n. 4, p. 564, doi. 10.1093/bioinformatics/btw646

By:

Zea, Diego J.;
Anfossi, Diego;
Nielsen, Morten;
Marino-Buslje, Cristina

Publication type:

Article

Accounting for pairwise distance restraints in FFT-based protein--protein docking.

Published in:

Bioinformatics, 2016, v. 32, n. 21, p. 3342, doi. 10.1093/bioinformatics/btw306

By:

Bing Xia;
Vajda, Sandor;
Kozakov, Dima

Publication type:

Article

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.

Published in:

Bioinformatics, 2016, v. 32, n. 21, p. 3270, doi. 10.1093/bioinformatics/btw404

By:

Krupa, Paweł;
Mozolewska, Magdalena A.;
Wiśniewska, Marta;
Yanping Yin;
Yi He;
Sieradzan, Adam K.;
Ganzynkowicz, Robert;
Lipska, Agnieszka G.;
Karczyńska, Agnieszka;
Ślusarz, Magdalena;
Ślusarz, Rafał;
Giełdoń, Artur;
Czaplewski, Cezary;
Jagieła, Dawid;
Zaborowski, Bartłomiej;
Scheraga, Harold A.;
Liwo, Adam

Publication type:

Article

Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking.

Published in:

Bioinformatics, 2016, v. 32, n. 16, p. 2451, doi. 10.1093/bioinformatics/btw197

By:

Daisuke Kuroda;
Gray, Jeffrey J.

Publication type:

Article

mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories.

Published in:

Bioinformatics, 2016, v. 32, n. 16, p. 2531, doi. 10.1093/bioinformatics/btw129

By:

Kota Kasahara;
Neetha Mohan;
Ikuo Fukuda;
Haruki Nakamura

Publication type:

Article

PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm.

Published in:

Bioinformatics, 2016, v. 32, n. 15, p. 2289, doi. 10.1093/bioinformatics/btw133

By:

Zaidman, Daniel;
Wolfson, Haim J.

Publication type:

Article

LIBRA: LIgand Binding site Recognition Application.

Published in:

Bioinformatics, 2015, v. 31, n. 24, p. 4020, doi. 10.1093/bioinformatics/btv489

By:

Hung, Le Viet;
Caprari, Silvia;
Bizai, Massimiliano;
Toti, Daniele;
Polticelli, Fabio

Publication type:

Article

svviz: a read viewer for validating structural variants.

Published in:

Bioinformatics, 2015, v. 31, n. 24, p. 3994, doi. 10.1093/bioinformatics/btv478

By:

Spies, Noah;
Zook, Justin M.;
Salit, Marc;
Sidow, Arend

Publication type:

Article

InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite.

Published in:

Bioinformatics, 2015, v. 31, n. 24, p. 4023, doi. 10.1093/bioinformatics/btv492

By:

Schenkelberg, Christian D.;
Bystroff, Christopher

Publication type:

Article

BiopLib and BiopTools--a C programming library and toolset for manipulating protein structure.

Published in:

Bioinformatics, 2015, v. 31, n. 24, p. 4017, doi. 10.1093/bioinformatics/btv482

By:

Porter, Craig T.;
Martin, Andrew C. R.

Publication type:

Article