ArticleNucleic acids research2004
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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
90 citing papers in PubMed.
- KIBRA anchoring the action of PKMζ maintains the persistence of memory.Science advances · 2024Article
- Graphene BioFET sensors for SARS-CoV-2 detection: a multiscale simulation approach.Nanoscale advances · 2022Article
- Molecular basis of crosstalk in nuclear receptors: heterodimerization between PXR and CAR and the implication in gene regulation.Nucleic acids research · 2022Article
- Article
- Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization.Biomolecules · 2019Article
- 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients.PLoS computational biology · 2019Article
- Article
- An effector from the Huanglongbing-associated pathogen targets citrus proteases.Nature communications · 2018Article
- Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- An in silico strategy for identification of novel drug targets against Plasmodium falciparum.Parasitology research · 2017Article
- Genome-wide associations of CD46 and IFI44L genetic variants with neutralizing antibody response to measles vaccine.Human genetics · 2017Article
- Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites.Nature genetics · 2017Article
- UNcleProt (Universal Nuclear Protein database of barley): The first nuclear protein database that distinguishes proteins from different phases of the cell cycle.Nucleus (Austin, Tex.) · 2017Article
- Robust classification of protein variation using structural modelling and large-scale data integration.Nucleic acids research · 2016Article
- The neuronal porosome complex in health and disease.Experimental biology and medicine (Maywood, N.J.) · 2016Review
- Article
- Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity.PLoS computational biology · 2015Article
- Computational Studies of Benzoxazinone Derivatives as Antiviral Agents against Herpes Virus Type 1 Protease.Molecules (Basel, Switzerland) · 2015Article
- Allosteric regulation of focal adhesion kinase by PIP₂ and ATP.Biophysical journal · 2015Article
- Antiprotozoal Nitazoxanide Derivatives: Synthesis, Bioassays and QSAR Study Combined with Docking for Mechanistic Insight.Current computer-aided drug design · 2015Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).
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.