Citation Impact
Citing Papers
Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy
2012 StandoutScienceNobel
Protein homology detection by HMM–HMM comparison
2004 Standout
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
2011
Improved de novo structure prediction in CASP 11 by incorporating coevolution information into Rosetta
2015 StandoutNobel
Protein structure determination using metagenome sequence data
2017 StandoutScienceNobel
Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction
2010 StandoutScienceNobel
Two Regions in the N-terminal Domain of Ionotropic Glutamate Receptor 3 Form the Subunit Oligomerization Interfaces That Control Subtype-specific Receptor Assembly
2005
A simple and fast heuristic for protein structure comparison
2008
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
2013
Structure of a mammalian ryanodine receptor
2014 StandoutNatureNobel
MODBASE, a database of annotated comparative protein structure models
2000
Structure of the TRPA1 ion channel suggests regulatory mechanisms
2015 StandoutNatureNobel
Within the twilight zone: a sensitive profile-profile comparison tool based on information theory
2002 StandoutNobel
Detection of reliable and unexpected protein fold predictions using 3D-Jury
2003
De Novo Prediction of Three-dimensional Structures for Major Protein Families
2002 StandoutNobel
Improved molecular replacement by density- and energy-guided protein structure optimization
2011 StandoutNatureNobel
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
2007 StandoutNobel
What is the value added by human intervention in protein structure prediction?
2001
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis
2002
NMR structure of the mouse prion protein domain PrP(121–231)
1996 StandoutNatureNobel
Structural basis for the recognition of hydroxyproline in HIF-1α by pVHL
2002 StandoutNatureNobel
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties11Edited by B. Honig
2001
Prediction of CASP6 structures using automated robetta protocols
2005 StandoutNobel
Channel opening and gating mechanism in AMPA-subtype glutamate receptors
2017 StandoutNatureNobel
The Protein Data Bank
2000 Standout
Combination of threading potentials and sequence profiles improves fold recognition 1 1Edited by B. Honig
2000
Shape complementarity at protein–protein interfaces
1994
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome
2013 StandoutNatureNobel
Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation
2003 StandoutNobel
Analysis and assessment of comparative modeling predictions in CASP4
2001
From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions
1999
De novo protein design. I. in search of stability and specificity
1999 StandoutNobel
Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment
2005
Identification of correct regions in protein models using structural, alignment, and consensus information
2006
Improving the quality of twilight‐zone alignments
2000
Automated prediction of CASP-5 structures using the Robetta server
2003 StandoutNobel
GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences
1999
Target selection for structural genomics.
2000
New CRISPR–Cas systems from uncultivated microbes
2016 StandoutNatureNobel
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
2002
Accurate design of co-assembling multi-component protein nanomaterials
2014 StandoutNatureNobel
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III
2011 StandoutNatureNobel
MUSCLE: multiple sequence alignment with high accuracy and high throughput
2004 Standout
Principles for designing ideal protein structures
2012 StandoutNatureNobel
Stochastic pairwise alignments
2002
Comparison of sequence profiles. Strategies for structural predictions using sequence information
2000
Completeness in structural genomics.
2001
Rosetta in CASP4: Progress in ab initio protein structure prediction
2001 StandoutNobel
Enhanced genome annotation using structural profiles in the program 3D-PSSM 1 1Edited by J. Thornton
2000
Protein structure prediction: when is it useful?
2009
MODBASE, a database of annotated comparative protein structure models
2002
Protein structure modeling for structural genomics.
2000
High-resolution structure prediction and the crystallographic phase problem
2007 StandoutNatureNobel
The HHpred interactive server for protein homology detection and structure prediction
2005 Standout
FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6
2005
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human
2009
FFAS03: a server for profile-profile sequence alignments
2005
Searching protein structure databases has come of age
1994
Large-scale comparison of protein sequence alignment algorithms with structure alignments
2000
Predicting protein structures with a multiplayer online game
2010 StandoutNatureNobel
Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller
2003
Super-resolution biomolecular crystallography with low-resolution data
2010 StandoutNatureNobel
The immune response of Drosophila
2003 StandoutNatureNobel
Kemp elimination catalysts by computational enzyme design
2008 StandoutNatureNobel
Surprising similarities in structure comparison
1996
Contact order and ab initio protein structure prediction
2002 StandoutNobel
Improved protein structure prediction using potentials from deep learning
2020 StandoutNatureNobel
PatchDock and SymmDock: servers for rigid and symmetric docking
2005 Standout
Alignment of protein sequences by their profiles
2004
Prospects for ab initio protein structural genomics
2001 StandoutNobel
De novo design of a fluorescence-activating β-barrel
2018 StandoutNatureNobel
Protein structure prediction and analysis using the Robetta server
2004 StandoutNobel
Prediction of local structure in proteins using a library of sequence-structure motifs
1998 StandoutNobel
Multi-Organ Characterization of Mitochondrial Genomic Rearrangements in Ad Libitum and Caloric Restricted Mice Show Striking Somatic Mitochondrial DNA Rearrangements with Age
1997
A diverse range of gene products are effectors of the type I interferon antiviral response
2011 StandoutNatureNobel
Refinement of homology‐based protein structures by molecular dynamics simulation techniques
2003
Structural genomics: beyond the Human Genome Project
1999
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
2006 StandoutNobel
Consensus alignment server for reliable comparative modeling with distant templates
2004
Quantitative reactivity profiling predicts functional cysteines in proteomes
2010 StandoutNatureNobel
Generalized comparative modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement
2001
Structure of the zinc-binding domain of an essential component of the hepatitis C virus replicase
2005 StandoutNatureNobel
Mechanism of folding chamber closure in a group II chaperonin
2010 StandoutNatureNobel
The Phyre2 web portal for protein modeling, prediction and analysis
2015 Standout
Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation
2011 StandoutNatureNobel
CASP5 assessment of fold recognition target predictions
2003
Scoring function for automated assessment of protein structure template quality
2004 Standout
Improved beta‐protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
2006 StandoutNobel
A surprising simplicity to protein folding
2000 StandoutNatureNobel
Comparison of X‐ray and NMR structures: Is there a systematic difference in residue contacts between X‐ray‐ and NMR‐resolved protein structures?
2005
Protein 3D Structure Computed from Evolutionary Sequence Variation
2011
Computational design of ligand-binding proteins with high affinity and selectivity
2013 StandoutNatureNobel
The PSIPRED protein structure prediction server
2000 Standout
ModBase, a database of annotated comparative protein structure models, and associated resources
2010
Critical assessment of methods of protein structure prediction (CASP)—Round 6
2005
New algorithms and an in silico benchmark for computational enzyme design
2006 StandoutNobel
Sixty-five years of the long march in protein secondary structure prediction: the final stretch?
2016
Comparative protein structure modeling by iterative alignment, model building and model assessment
2003
Pcons5: combining consensus, structural evaluation and fold recognition scores
2005
A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction
2005
Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
2012
Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment
2003
Exploitation of binding energy for catalysis and design
2009 StandoutNatureNobel
Structure Comparison and Structure Patterns
2000
Accurate design of megadalton-scale two-component icosahedral protein complexes
2016 StandoutScienceNobel
Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
1999
Critical assessment of methods of protein structure prediction (CASP)-round V
2003
Ab Initio Protein Structure Prediction: Progress and Prospects
2001 StandoutNobel
Mutation of the mouse klotho gene leads to a syndrome resembling ageing.
1997 Standout
3D-Hit: fast structural comparison of proteins.
2002
Crystal Structure of Human BPI and Two Bound Phospholipids at 2.4 Angstrom Resolution
1997 Science
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
2005 Standout
Toward High-Resolution de Novo Structure Prediction for Small Proteins
2005 StandoutScienceNobel
The new frontier of genome engineering with CRISPR-Cas9
2014 StandoutScienceNobel
APDB: a novel measure for benchmarking sequencealignment methods without reference alignments
2003
Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel
2008
Fast overlapping of protein contact maps by alignment of eigenvectors
2010
Ab initio protein structure prediction of CASP III targets using ROSETTA
1999 StandoutNobel
Recent improvements in prediction of protein structure by global optimization of a potential energy function
2001
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
2003 StandoutScienceNobel
Fold prediction by a hierarchy of sequence, threading, and modeling methods
1998
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
1998
Comparative Protein Structure Modeling of Genes and Genomes
2000 Standout
A family of human receptors structurally related to Drosophila Toll
1998 Standout
Protein Structure Prediction and Structural Genomics
2001 StandoutScienceNobel
Global Optimization of Clusters, Crystals, and Biomolecules
1999 Science
Mapping the Protein Universe
1996 Science
Prediction of membrane protein structures with complex topologies using limited constraints
2009 StandoutNobel
Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
2011 StandoutScienceNobel
De Novo Computational Design of Retro-Aldol Enzymes
2008 StandoutScienceNobel
Design of a hyperstable 60-subunit protein icosahedron
2016 StandoutNatureNobel
Coupled prediction of protein secondary and tertiary structure
2003 StandoutNobel
Protein structure prediction for the male-specific region of the human Y chromosome
2004 StandoutNobel
Phylogenetic Perspectives in Innate Immunity
1999 StandoutScienceNobel
Comparative Protein Structure Modeling Using Modeller
2006 Standout
Comparison of proteins based on segments structural similarity.
2004
Works of Daniel Fischer being referenced
A study of quality measures for protein threading models
2001
Fold-recognition detects an error in the Protein Data Bank
2002
A computer vision based technique for 3-D sequence-independent structural comparison of proteins
1993
Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures
1996
Finding families for genomic ORFans
1999
An Efficient Automated Computer Vision Based Technique for Detection of Three Dimensional Structural Motifs in Proteins
1992
LiveBench-2: Large-scale automated evaluation of protein structure prediction servers
2001
A geometry-based suite of moleculardocking processes
1995
Structure prediction meta server
2001
Protein fold recognition using sequence‐derived predictions
1996
MaxSub: an automated measure for the assessment of protein structure prediction quality
2000
Molecular surface recognition by a computer vision-based technique
1994
Servers for protein structure prediction
2006
LiveBench-6: Large-scale automated evaluation of protein structure prediction servers
2003
The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2
2000
CAFASP3: The third critical assessment of fully automated structure prediction methods
2003
3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor
2003
Rational structural genomics: affirmative action for ORFans and the growth in our structural knowledge
1999
Increased frequency of deletions in the mitochondrial genome with age ofCaenorhabditis elegans
1995
A 3D sequence-independent representation of the protein data bank
1995
CAFASP2: The second critical assessment of fully automated structure prediction methods
2001
3D-Jury: a simple approach to improve protein structure predictions
2003
LiveBench‐8: The large‐scale, continuous assessment of automated protein structure prediction
2004
A study of combined structure/sequence profiles
1996
CAFASP‐1: Critical assessment of fully automated structure prediction methods
1999
Hybrid Fold Recognition: Combining Sequence Derived Properties with Evolutionary Information
1999
Modeling three-dimensional protein structures for amino acid sequences of the CASP3 experiment using sequence-derived predictions
1999
Assessing the performance of fold recognition methods by means of a comprehensive benchmark.
1996
Assigning amino acid sequences to 3‐dimensional protein folds
1996
Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium
1997
LiveBench‐1: Continuous benchmarking of protein structure prediction servers
2001
CAFASP-1: Critical assessment of fully automated structure prediction methods
1999