ArticleBMC bioinformatics2010
Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins.International journal of molecular sciences · 2023Article
- Improving classification of correct and incorrect protein-protein docking models by augmenting the training set.Bioinformatics advances · 2023Article
- Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Computational Ways to Enhance Protein Inhibitor Design.Frontiers in molecular biosciences · 2020Article
- Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change.Biophysical journal · 2017Article
- Knowledge-based entropies improve the identification of native protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Distributions of experimental protein structures on coarse-grained free energy landscapes.The Journal of chemical physics · 2015Article
- GENN: a GEneral Neural Network for learning tabulated data with examples from protein structure prediction.Methods in molecular biology (Clifton, N.J.) · 2015Article
- The scoring of poses in protein-protein docking: current capabilities and future directions.BMC bioinformatics · 2013Article
- Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.PLoS computational biology · 2012Article
- Biophysical and structural considerations for protein sequence evolution.BMC evolutionary biology · 2011Article
- Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.Journal of structural and functional genomics · 2011Article
- Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models.Proteins · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundKnowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online.
resultsOur new knowledge-based potential server makes available many of these potentials for easy use to automatically compute the energies of protein structures or models supplied. Our web server for protein energy estimation uses four-body potentials, short-range potentials, and 23 different two-body potentials. Users can select potentials according to their needs and preferences. Files containing the coordinates of protein atoms in the PDB format can be uploaded as input. The results will be returned to the user's email address.
conclusionsOur Potentials 'R' Us server is an easily accessible, freely available tool with a web interface that collects all existing and future protein coarse-grained potentials and computes energies of multiple structural models.
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