ArticleBMC bioinformatics2010
New statistical potential for quality assessment of protein models and a survey of energy functions.
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 43 papers.
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Who cites it
43 citing papers in PubMed.
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
- lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures.Journal of chemical information and modeling · 2024Article
- lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures.bioRxiv : the preprint server for biology · 2024Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation.NAR genomics and bioinformatics · 2023Article
- On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations.Antibodies (Basel, Switzerland) · 2022Article
- Structure-conditioned amino-acid couplings: How contact geometry affects pairwise sequence preferences.Protein science : a publication of the Protein Society · 2022Article
- Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV.PLoS computational biology · 2022Article
- rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.Biophysical journal · 2022Article
- A novel algorithm for ranking RNA structure candidates.Biophysical journal · 2022Article
- SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions.BMC bioinformatics · 2021Article
- A knowledge-based scoring function to assess quaternary associations of proteins.Bioinformatics (Oxford, England) · 2020Article
- Article
- Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling.PLoS computational biology · 2019Article
- A simple neural network implementation of generalized solvation free energy for assessment of protein structural models.RSC advances · 2019Article
- ANDIS: an atomic angle- and distance-dependent statistical potential for protein structure quality assessment.BMC bioinformatics · 2019Article
- Methods for the Refinement of Protein Structure 3D Models.International journal of molecular sciences · 2019Review
- Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning.PLoS computational biology · 2019Article
- Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model.Biophysical journal · 2018Article
- Protein structure prediction.International journal of modern physics. B · 2018Article
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2 authors.
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Abstract
backgroundScoring functions, such as molecular mechanic forcefields and statistical potentials are fundamentally important tools in protein structure modeling and quality assessment.
resultsThe performances of a number of publicly available scoring functions are compared with a statistical rigor, with an emphasis on knowledge-based potentials. We explored the effect on accuracy of alternative choices for representing interaction center types and other features of scoring functions, such as using information on solvent accessibility, on torsion angles, accounting for secondary structure preferences and side chain orientation. Partially based on the observations made, we present a novel residue based statistical potential, which employs a shuffled reference state definition and takes into account the mutual orientation of residue side chains. Atom- and residue-level statistical potentials and Linux executables to calculate the energy of a given protein proposed in this work can be downloaded from http://www.fiserlab.org/potentials.
conclusionsAmong the most influential terms we observed a critical role of a proper reference state definition and the benefits of including information about the microenvironment of interaction centers. Molecular mechanical potentials were also tested and found to be over-sensitive to small local imperfections in a structure, requiring unfeasible long energy relaxation before energy scores started to correlate with model quality.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.