Search Results

MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts.

• Authors : Philipp M; Image and Signal Processing Group, Department of Computer Science, Leipzig University, Augustusplatz 10, 04109 Leipzig, Germany.; Moth CW

Subjects: Internet* ; Software* ; Mutation*

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W132-W139.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium:

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Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families.

• Authors : Parra RG; Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.; Freiberger MI

Subjects: Software* ; Protein Folding* ; Internet*

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W233-W237.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium:

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The Damietta Server: a comprehensive protein design toolkit.

• Authors : Grin I; Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany.; Maksymenko K

Subjects: Software* ; Proteins*/Proteins*/Proteins*/chemistry ; Internet*

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W200-W206.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium:

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Deep learning for the PSIPRED Protein Analysis Workbench.

• Authors : Buchan DWA; UCL Bioinformatics Group, Department of Computer Science, University College London, London, WC1E 6BT, UK.; Moffat L

Subjects: Deep Learning* ; Software* ; Proteins*/Proteins*/Proteins*/chemistry

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W287-W293.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium:

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GPSFun: geometry-aware protein sequence function predictions with language models.

• Authors : Yuan Q; School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, Guangdong 510000, China.; Tian C

Subjects: Software* ; Proteins*/Proteins*/Proteins*/chemistry ; Proteins*/Proteins*/Proteins*/metabolism

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W248-W255.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium:

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A curated rotamer library for common post-translational modifications of proteins.

• Authors : Zhang O; Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA 94720, United States.; Naik SA

Subjects: Protein Processing, Post-Translational* ; Proteins*/Proteins*/Proteins*/chemistry ; Proteins*/Proteins*/Proteins*/metabolism

• Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Jul 01; Vol. 40 (7).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium:

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Efficient protein structure archiving using ProteStAr.

• Authors : Deorowicz S; Department of Algorithmics and Software, Silesian University of Technology, Akademicka 16, Gliwice, PL-44100, Poland.; Gudyś A

Subjects: Databases, Protein* ; Proteins*/Proteins*/Proteins*/chemistry ; Software*

• Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Jul 01; Vol. 40 (7).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium:

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Surface-based multimodal protein-ligand binding affinity prediction.

• Authors : Xu S; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China.; Shen L

Subjects: Proteins*/Proteins*/Proteins*/metabolism ; Proteins*/Proteins*/Proteins*/chemistry ; Protein Binding*

• Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Jul 01; Vol. 40 (7).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium:

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RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.

• Authors : Bittrich S; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, United States.; Segura J

Subjects: Databases, Protein* ; Proteins*/Proteins*/Proteins*/chemistry ; Software*

• Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Jun 03; Vol. 40 (6).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium:

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MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2.

• Authors : Chim HY; Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, Stockholm 106 91, Sweden.; Elofsson A

Subjects: Monte Carlo Method* ; Algorithms* ; Software*

• Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Jun 03; Vol. 40 (6).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium:

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Multilevel superposition for deciphering the conformational variability of protein ensembles.

• Authors : Amisaki T; Department of Biological Regulation, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan.

Subjects: Proteins*/Proteins*/Proteins*/chemistry ; Molecular Dynamics Simulation*; Protein Conformation

• Source: Briefings in bioinformatics [Brief Bioinform] 2024 Mar 27; Vol. 25 (3).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium:

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GSScore: a novel Graphormer-based shell-like scoring method for protein-ligand docking.

• Authors : Guo L; School of Computer Science and Engineering, Central South University, Rd. Lu Shan Nan, 410083, Changsha, P.R. China.; Hunan Provincial Key Lab on Bioinformatics, Central South University, Rd. Lu Shan Nan, 410083, Changsha, P.R. China.

Subjects: Proteins*/Proteins*/Proteins*/chemistry ; Proteins*/Proteins*/Proteins*/metabolism ; Molecular Docking Simulation*

• Source: Briefings in bioinformatics [Brief Bioinform] 2024 Mar 27; Vol. 25 (3).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium:

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Structure prediction of linear and cyclic peptides using CABS-flex.

• Authors : Badaczewska-Dawid A; Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, 50011 IA, USA.; Wróblewski K

Subjects: Peptides, Cyclic* ; Proteins*/Proteins*/Proteins*/chemistry; Peptides/Peptides/Peptides/chemistry

• Source: Briefings in bioinformatics [Brief Bioinform] 2024 Jan 22; Vol. 25 (2).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium:

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Enhancing protein dynamics analysis with hydrophilic polyethylene glycol cross-linkers.

• Authors : Sun M; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei 430071, China.; University of Chinese Academy of Sciences, Beijing 100039, China.

Subjects: Polyethylene Glycols*/Polyethylene Glycols*/Polyethylene Glycols*/chemistry ; Proteins*/Proteins*/Proteins*/chemistry; Mass Spectrometry

• Source: Briefings in bioinformatics [Brief Bioinform] 2024 Jan 22; Vol. 25 (2).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium:

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ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era.

• Authors : Špačková A; Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic.; Vávra O

Subjects: Databases, Protein* ; Proteins*/Proteins*/Proteins*/chemistry ; Software*

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jan 05; Vol. 52 (D1), pp. D413-D418.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium:

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DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.

• Authors : Lee JW; Department of Computer Science, Hanyang University, Seoul 04763, Korea.; Center for Advanced Computation, Korea Institute for Advanced Study, Seoul 02455, Korea.

Subjects: Proteins*/Proteins*/Proteins*/chemistry ; Software*; Protein Conformation

• Source: Bioinformatics (Oxford, England) [Bioinformatics] 2023 Dec 01; Vol. 39 (12).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium:

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Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.

• Authors : Wang T; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.; Wang L

Subjects: Proteins*/Proteins*/Proteins*/chemistry; Protein Conformation

• Source: Briefings in bioinformatics [Brief Bioinform] 2023 Nov 22; Vol. 25 (1).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium:

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AFsample: improving multimer prediction with AlphaFold using massive sampling.

• Authors : Wallner B; Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden.

Subjects: Proteins*/Proteins*/Proteins*/chemistry ; Neural Networks, Computer*; Protein Conformation

• Source: Bioinformatics (Oxford, England) [Bioinformatics] 2023 Sep 02; Vol. 39 (9).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium:

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Agricola

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GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations.

• Authors : Rademaker DT; Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.; van Geemen KJ

Subjects: Proteins*/Proteins*/Proteins*/chemistry ; Software*; Protein Conformation

• Source: Bioinformatics (Oxford, England) [Bioinformatics] 2023 Aug 01; Vol. 39 (8).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium:

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Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling.

• Authors : Maddhuri Venkata Subramaniya SR; Department of Computer Science, Purdue University, West Lafayette, IN 47907, United States.; Terashi G

Subjects: Proteins*/Proteins*/Proteins*/chemistry; Cryoelectron Microscopy ; Models, Molecular

• Source: Bioinformatics (Oxford, England) [Bioinformatics] 2023 Aug 01; Vol. 39 (8).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium:

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EnGens: a computational framework for generation and analysis of representative protein conformational ensembles.

• Authors : Conev A; Department of Computer Science, Rice University, Houston 77005, TX, USA.; Rigo MM

Subjects: Molecular Dynamics Simulation* ; Proteins*/Proteins*/Proteins*/chemistry; Protein Conformation

• Source: Briefings in bioinformatics [Brief Bioinform] 2023 Jul 20; Vol. 24 (4).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium:

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GraphGPSM: a global scoring model for protein structure using graph neural networks.

• Authors : He G; College of Information Engineering, Zhejiang University of Technology.; Liu J

Subjects: Algorithms* ; Proteins*/Proteins*/Proteins*/chemistry; Protein Conformation

• Source: Briefings in bioinformatics [Brief Bioinform] 2023 Jul 20; Vol. 24 (4).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium:

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αCharges: partial atomic charges for AlphaFold structures in high quality.

• Authors : Schindler O; CEITEC - Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.

Subjects: Software* ; Proteins*/Proteins*/Proteins*/chemistry ; Computational Biology*/Computational Biology*/Computational Biology*/instrumentation

• Source: Nucleic acids research [Nucleic Acids Res] 2023 Jul 05; Vol. 51 (W1), pp. W11-W16.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium:

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Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers.

• Authors : McGuffin LJ; School of Biological Sciences, University of Reading, Whiteknights, ReadingRG6 6EX, UK.; Edmunds NS

Subjects: Software* ; Proteins*/Proteins*/Proteins*/chemistry; Ligands

• Source: Nucleic acids research [Nucleic Acids Res] 2023 Jul 05; Vol. 51 (W1), pp. W274-W280.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium:

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