Standout Papers
Citation Impact
Citing Papers
Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation
2004 StandoutNobel
An enumerative algorithm for de novo design of proteins with diverse pocket structures
2020 StandoutNobel
Nature of the protein universe
2009 StandoutNobel
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
2016 StandoutScience
Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
2012
The protein structure prediction problem could be solved using the current PDB library
2005
Global analysis of protein folding using massively parallel design, synthesis, and testing
2017 StandoutScienceNobel
De novo design of transmembrane β barrels
2021 StandoutScienceNobel
Computational design of a protein crystal
2012
The origin of β-strand bending in globular proteins
2015
Function and Structure of a Prokaryotic Formylglycine-generating Enzyme
2008 StandoutNobel
Comparative mapping of sequence-based and structure-based protein domains
2005
PROMALS3D: a tool for multiple protein sequence and structure alignments
2008
CATH – a hierarchic classification of protein domain structures
1997 Standout
Estimating the number of protein folds and families from complete genome data 1 1Edited by J. Thornton
2000
De Novo Prediction of Three-dimensional Structures for Major Protein Families
2002 StandoutNobel
Domain Tree-Based Analysis of Protein Architecture Evolution
2007
Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures
2005 StandoutNobel
The Highly Cooperative Folding of Small Naturally Occurring Proteins Is Likely the Result of Natural Selection
2007 StandoutNobel
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
2015 Standout
COACH: profile–profile alignment of protein families using hidden Markov models
2004
Protein structure prediction on the Web: a case study using the Phyre server
2009 Standout
Align-m—a new algorithm for multiple alignment of highly divergent sequences
2004
The Protein Data Bank
2000 Standout
Sulfatases: Structure, Mechanism, Biological Activity, Inhibition, and Synthetic Utility
2004
Design of an optimal Chebyshev‐expanded discrimination function for globular proteins
2002 StandoutNobel
A Double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms
2008 StandoutNobel
Analysis of class I introns in a mitochondrial plasmid associated with senescence of Podospora anserina reveals extraordinary resemblance to the Tetrahymena ribosomal intron
1985
SCOP database in 2004: refinements integrate structure and sequence family data
2003
Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion
2014
On the design and analysis of protein folding potentials
2000
Pervasive generation of oppositely oriented spacers during CRISPR adaptation
2014
SWISS-MODEL: an automated protein homology-modeling server
2003 Standout
JPred4: a protein secondary structure prediction server
2015
Touring protein fold space with Dali/FSSP
1998
New CRISPR–Cas systems from uncultivated microbes
2016 StandoutNatureNobel
Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity
2014 StandoutNobel
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
2002
New structure — novel fold?
1997
Functional Inferences from Blind ab Initio Protein Structure Predictions
2001 StandoutNobel
Thoroughly sampling sequence space: Large‐scale protein design of structural ensembles
2002
The number of protein folds and their distribution over families in nature
2003
Supra-domains: Evolutionary Units Larger than Single Protein Domains
2003
Insights into Wnt binding and signalling from the structures of two Frizzled cysteine-rich domains
2001 Nature
A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins
2012
The guanosine binding site of the Tetrahymena ribozyme
1989 StandoutNatureNobel
TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins
2016 StandoutNobel
MUSCLE: multiple sequence alignment with high accuracy and high throughput
2004 Standout
The ASTRAL Compendium in 2004
2003
Domain Rearrangements in Protein Evolution
2005
Rapid protein domain assignment from amino acid sequence using predicted secondary structure
2002
COMPASS: A Tool for Comparison of Multiple Protein Alignments with Assessment of Statistical Significance
2003
Comparison of sequence profiles. Strategies for structural predictions using sequence information
2000
Completeness in structural genomics.
2001
Identification, function and structure of the mycobacterial sulfotransferase that initiates sulfolipid-1 biosynthesis
2004 StandoutNobel
Protein structure prediction: when is it useful?
2009
Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony
2006
Direct Evidence for ArOS Bond Cleavage upon Inactivation of Pseudomonas aeruginosa Arylsulfatase by Aryl Sulfamates
2008
MODBASE, a database of annotated comparative protein structure models
2002
Rational design of α-helical tandem repeat proteins with closed architectures
2015 StandoutNatureNobel
Protein structure modeling for structural genomics.
2000
Structural genomics and its importance for gene function analysis
2000
Hidden Markov models
1996
Sulfotransferases: Structure, Mechanism, Biological Activity, Inhibition, and Synthetic Utility
2004
UCSF Chimera—A visualization system for exploratory research and analysis
2004 Standout
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
2011 Standout
A unifold, mesofold, and superfold model of protein fold use
2001
Design, Production and Molecular Structure of a New Family of Artificial Alpha-helicoidal Repeat Proteins (αRep) Based on Thermostable HEAT-like Repeats
2010
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis
2016
Large-scale comparison of protein sequence alignment algorithms with structure alignments
2000
Sequence-based prediction of protein domains
2004
ECOD: An Evolutionary Classification of Protein Domains
2014
LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells
2012
A comparison of scoring functions for protein sequence profile alignment
2004
EVEREST: automatic identification and classification of protein domains in all protein sequences
2006
Surprising similarities in structure comparison
1996
The Generation of New Protein Functions by the Combination of Domains
2007
Protein-RNA networks revealed through covalent RNA marks
2015
Pfam 10 years on: 10 000 families and still growing
2008
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds
2006
Estimating the number of protein folds
1998
The Solution Structure of the S1 RNA Binding Domain: A Member of an Ancient Nucleic Acid–Binding Fold
1997
Structural genomics: beyond the Human Genome Project
1999
Design of metalloproteins and novel protein folds using variational autoencoders
2018
The structure of the protein universe and genome evolution
2002 Nature
Template-based modeling and free modeling by I-TASSER in CASP7
2007
Drosophila Hrp48 Is Required for Mushroom Body Axon Growth, Branching and Guidance
2015
A ‘periodic table’ for protein structures
2002 Nature
TM-align: a protein structure alignment algorithm based on the TM-score
2005 Standout
Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity
2015 StandoutNatureNobel
The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure
2005
Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
1997
Drug Targets in Mycobacterial Sulfur Metabolism
2007
Progress of Structural Genomics Initiatives: An Analysis of Solved Target Structures
2005
How representative are the known structures of the proteins in a complete genome? A comprehensive structural census
1998
CAFASP‐1: Critical assessment of fully automated structure prediction methods
1999
De novo protein design: how do we expand into the universe of possible protein structures?
2015
Prediction of functionally important residues based solely on the computed energetics of protein structure 1 1Edited by B. Honig
2001
Toward Consistent Assignment of Structural Domains in Proteins
2004
Aryl sulfamates are broad spectrum inactivators of sulfatases: Effects on sulfatases from various sources
2008
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
1998
Sulfate Metabolism in Mycobacteria
2006 StandoutNobel
Selenium incorporation using recombinant techniques
2010
PDBsum: a web-based database of summaries and analyses of all PDB structures
1997
A General Computational Approach for Repeat Protein Design
2014 StandoutNobel
Molecular Basis for G Protein Control of the Prokaryotic ATP Sulfurylase
2006 StandoutNobel
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
1997 Standout
An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins
2017
Structure Comparison and Structure Patterns
2000
Sulfatase-activated fluorophores for rapid discrimination of mycobacterial species and strains
2013 StandoutNobel
Growth of novel protein structural data
2007 StandoutNobel
FOLD HELICAL PROTEINS BY ENERGY MINIMIZATION IN DIHEDRAL SPACE AND A DFIRE-BASED STATISTICAL ENERGY FUNCTION
2005
Near-native structure refinement using in vacuo energy minimization
2007 StandoutNobel
A model for the RNA-catalyzed replication of RNA.
1986 StandoutNobel
Sites of circularization of theTetrahymenarRNA IVS are determined by sequence and influenced by position and secondary structure
1985 StandoutNobel
β‐Bulges: Extensive structural analyses of β‐sheets irregularities
2013
Defining the Inside and Outside of a Catalytic RNA Molecule
1989 StandoutScienceNobel
Sinorhizobium meliloti Sulfotransferase That Modifies Lipopolysaccharide
2004
Self-catalyzed cyclization of the intervening sequence RNA ofTetrahymena:inhibition by methidiumpropyl-EDTA and localization of the major dye binding sites
1985 StandoutNobel
Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase.
1985 StandoutNobel
Packing helices in proteins by global optimization of a potential energy function
2003
Novel folded protein domains generated by combinatorial shuffling of polypeptide segments
2000 StandoutNobel
PDBsum: Structural summaries of PDB entries
2017
Self-Splicing RNA: Implications for Evolution
1985 StandoutNobel
Protein engineering by highly parallel screening of computationally designed variants
2016
Toward High-Resolution de Novo Structure Prediction for Small Proteins
2005 StandoutScienceNobel
Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro
1986
RNA-Seq Analysis Identifies a Novel Set of Editing Substrates for Human ADAR2 Present in Saccharomyces cerevisiae
2013
Lysosomal cathepsin D mediates endogenous mucin glycodomain catabolism in mammals
2022 StandoutNobel
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment
2004
Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
2001
One binding site determines sequence specificity of Tetrahymena pre-rRNA self-splicing, trans-splicing, and RNA enzyme activity
1986 StandoutNobel
The tetrahymena rRNA intron self-splices in E. coli: In vivo evidence for the importance of key base-paired regions of RNA for RNA enzyme function
1985
TargetDB: a target registration database for structural genomics projects
2004
Funnel sculpting for in silico assembly of secondary structure elements of proteins
2003 StandoutNobel
MaxBench: evaluation of sequence and structure comparison methods
2002
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes
2018 StandoutScienceNobel
RNA structure, not sequence, determines the 5' splice-site specificity of a group I intron.
1989 StandoutNobel
Selection of circularization sites in a group I IVS RNA requires multiple alignments of an internal template-like sequence
1987 StandoutNobel
Estimating the total number of protein folds
1999
A sulfated metabolite produced bystf3negatively regulates the virulence ofMycobacteriumtuberculosis
2006 StandoutNobel
The Intervening Sequence RNA of Tetrahymena Is an Enzyme
1986 StandoutScienceNobel
Short motif sequences determine the targets of the prokaryotic CRISPR defence system
2009
General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH
2013 StandoutNobel
Solvent dramatically affects protein structure refinement
2008 StandoutNobel
MmpL8 is required for sulfolipid-1 biosynthesis and Mycobacterium tuberculosis virulence
2003 StandoutNobel
Generalized ensemble methods for de novo structure prediction
2009 StandoutNobel
Reversibility of cyclization of the tetrahymena rRNA intervening sequence: implication for the mechanism of splice site choice
1985 StandoutNobel
The Tetrahymena ribozyme acts like an RNA restriction endonuclease
1986 StandoutNatureNobel
Speculations on the early course of evolution.
1986
Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium
1997
Comparative Protein Structure Modeling of Genes and Genomes
2000 Standout
Protein Structure Prediction and Structural Genomics
2001 StandoutScienceNobel
RNA splicing in neurospora mitochondria: Self-splicing of a mitochondrial intron in vitro
1984
Mapping the Protein Universe
1996 Science
Effect of alphabet size and foldability requirements on protein structure designability
1999
Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation
2002
Control over overall shape and size in de novo designed proteins
2015 StandoutNobel
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
2012
Three-dimensional model of the active site of the self-splicing rRNA precursor of Tetrahymena.
1987 StandoutNobel
Sequence requirements for self-splicing of theTetrahymena thermophilapre-ribosomal RNA
1985 StandoutNobel
Protein topology and stability define the space of allowed sequences
2002 StandoutNobel
A structural census of the current population of protein sequences
1997 StandoutNobel
A unified statistical framework for sequence comparison and structure comparison
1998 StandoutNobel
Role of conserved sequence elements 9L and 2 in self-splicing of the Tetrahymena ribosomal RNA precursor
1986 StandoutNobel
Local sequence of protein β‐strands influences twist and bend angles
2014
Automatic classification of protein structure by using Gauss integrals
2002
Discovery of sulfated metabolites in mycobacteria with a genetic and mass spectrometric approach
2002 StandoutNobel
Mechanism of recognition of the 5′ splice site in self-splicing group I introns
1986 StandoutNatureNobel
Enzymatic activity of the conserved core of a group I self-splicing intron
1986 StandoutNatureNobel
Three variant introns of the same general class in the mitochondrial gene for cytochrome oxidase subunit 1 in Aspergillus nidulans.
1984
Intermolecular exon ligation of the rRNA precursor of tetrahymena: Oligonucleotides can function as 5′ exons
1985 StandoutNobel
A self-splicing RNA excises an intron lariat
1986
Works of Steven E. Brenner being referenced
Population statistics of protein structures
1997
Proceedings Of The Third International Conference On Intelligent Systems For Molecular Biology
1995
[37] Understanding protein structure: Using scop for fold interpretation
1996
A tour of structural genomics
2001
Target selection for structural genomics.
2000
SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures
2013
Sulfotransferases and Sulfatases in Mycobacteria
2002 StandoutNobel
Expectations from structural genomics
2000
The PRESAGE database for structural genomics
1999 StandoutNobel
The ASTRAL compendium for protein structure and sequence analysis
2000
WebLogo: A Sequence Logo Generator: Figure 1
2004 Standout
Errors in genome annotation
1999
Genome-wide Analysis of Alternative Pre-mRNA Splicing and RNA-Binding Specificities of the Drosophila hnRNP A/B Family Members
2009
Population statistics of protein structures: lessons from structural classifications
1997
Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches
2004
Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila
2005
PROTEIN FOLDS IN THE ALL-β AND ALL-α CLASSES
1997
Close relationship between certain nuclear and mitochondrial introns
1983
SCOP: a Structural Classification of Proteins database
1999
Distribution of Protein Folds in the Three Superkingdoms of Life
1999
The Impact of Structural Genomics: Expectations and Outcomes
2006 Science
SCOP: A structural classification of proteins database for the investigation of sequences and structures
1995 Standout
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
1998