ReviewBioinformatics and biology insights2016
PDBparam: Online Resource for Computing Structural Parameters of Proteins.
Review in Bioinformatics and biology insights, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it, 34 citations in OpenAlex.
- Current computational tools for protein lysine acylation site prediction.Briefings in bioinformatics · 2024Pooled it
- Using Domain Insertion to Create Sulfite Reductases That Present Chemical-Dependent Activities.ACS synthetic biology · 2026Article
- Plant-associated fungi co-opt ancient antimicrobials for host manipulation.Science advances · 2026Article
- A review on computational models for predicting protein solubility.Journal of microbiology (Seoul, Korea) · 2025Review
- A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase.Protein science : a publication of the Protein Society · 2023Article
- iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets.Nucleic acids research · 2022Article
- Fluorescent Imaging of Extracellular Fungal Enzymes Bound onto Plant Cell Walls.International journal of molecular sciences · 2022Article
- Elucidating important structural features for the binding affinity of spike - SARS-CoV-2 neutralizing antibody complexes.Proteins · 2022Article
- Antibacterial Activity of T22, a Specific Peptidic Ligand of the Tumoral Marker CXCR4.Pharmaceutics · 2021Article
- Residue Cluster Classes: A Unified Protein Representation for Efficient Structural and Functional Classification.Entropy (Basel, Switzerland) · 2020Article
- Biophysical Characterization Platform Informs Protein Scaffold Evolvability.ACS combinatorial science · 2019Article
- Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level.Global heart · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the structure-function relationship in proteins is a longstanding goal in molecular and computational biology. The development of structure-based parameters has helped to relate the structure with the function of a protein. Although several structural features have been reported in the literature, no single server can calculate a wide-ranging set of structure-based features from protein three-dimensional structures. In this work, we have developed a web-based tool, PDBparam, for computing more than 50 structure-based features for any given protein structure. These features are classified into four major categories: (i) interresidue interactions, which include short-, medium-, and long-range interactions, contact order, long-range order, total contact distance, contact number, and multiple contact index, (ii) secondary structure propensities such as α-helical propensity, β-sheet propensity, and propensity of amino acids to exist at various positions of α-helix and amino acid compositions in high B-value regions, (iii) physicochemical properties containing ionic interactions, hydrogen bond interactions, hydrophobic interactions, disulfide interactions, aromatic interactions, surrounding hydrophobicity, and buriedness, and (iv) identification of binding site residues in protein-protein, protein-nucleic acid, and protein-ligand complexes. The server can be freely accessed at http://www.iitm.ac.in/bioinfo/pdbparam/. We suggest the use of PDBparam as an effective tool for analyzing protein structures.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.