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List of works by Adam Godzik

A Blueprint for HIV Vaccine Discovery

scientific article

A Distinct Type of Pilus from the Human Microbiome

scientific article

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

scientific article

A Structural Basis for the Regulatory Inactivation of DnaA

scientific article

A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution

scientific article

A diverse family of proteins containing tumor necrosis factor receptor-associated factor domains

scientific article

A method for predicting protein structure from sequence.

scientific article

A method for the prediction of surface "U"-turns and transglobular connections in small proteins

scientific article published in February 1997

A novel PAAD-containing protein that modulates NF-kappa B induction by cytokines tumor necrosis factor-alpha and interleukin-1beta

scientific article

A novel enhancer of the Apaf1 apoptosome involved in cytochrome c-dependent caspase activation and apoptosis

scientific article (publication date: 23 March 2001)

A primer on metagenomics

scientific article

A residue in the S2 subsite controls substrate selectivity of matrix metalloproteinase-2 and matrix metalloproteinase-9.

scientific article published on 18 February 2003

A segment alignment approach to protein comparison.

scientific article

A support vector machine approach to the identification of phosphorylation sites

scientific article published in January 2005

A unique substrate binding mode discriminates membrane type-1 matrix metalloproteinase from other matrix metalloproteinases

scientific article published on 16 April 2002

A unique substrate recognition profile for matrix metalloproteinase-2.

scientific article

A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins

scientific article

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction.

scientific article

AIDA: ab initio domain assembly server

scientific article

ATP-activated oligomerization as a mechanism for apoptosis regulation: fold and mechanism prediction for CED-4.

scientific article published on May 2000

Aggregate formation and synaptic abnormality induced by DSCR1.

scientific article published in March 2004

AhpF can be dissected into two functional units: tandem repeats of two thioredoxin-like folds in the N-terminus mediate electron transfer from the thioredoxin reductase-like C-terminus to AhpC.

scientific article

An algorithm for prediction of structural elements in small proteins.

scientific article published in January 1996

Analysis of individual protein regions provides novel insights on cancer pharmacogenomics

scientific article

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

scientific article

Automatic detection of subsystem/pathway variants in genome analysis

scientific article published in June 2005

BAR: An apoptosis regulator at the intersection of caspases and Bcl-2 family proteins

scientific article

Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

scientific article

Basis for substrate recognition and distinction by matrix metalloproteinases

scientific article

Bcl-B, a novel Bcl-2 family member that differentially binds and regulates Bax and Bak

scientific article

Bcl-G, a novel pro-apoptotic member of the Bcl-2 family

scientific article

Between order and disorder in protein structures: analysis of "dual personality" fragments in proteins

scientific article published on September 2007

Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort

scientific article published on 14 January 2016

CADD, a Chlamydia protein that interacts with death receptors.

scientific article published on 22 January 2002

CAFASP-1: Critical assessment of fully automated structure prediction methods

article

CAFASP-1: critical assessment of fully automated structure prediction methods

scientific article (publication date: 1999)

CARD6 is a modulator of NF-kappa B activation by Nod1- and Cardiak-mediated pathways

scientific journal article

CARD8 and NLRP1 undergo autoproteolytic processing through a ZU5-like domain

scientific article

CLAN, a novel human CED-4-like gene

scientific article

Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets

Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets

scientific article published on 01 January 2019

Cancer3D: understanding cancer mutations through protein structures

scientific article

Characterization of matrix metalloproteinase-26, a novel metalloproteinase widely expressed in cancer cells of epithelial origin

scientific article (publication date: 15 June 2001)

Characterization of the anti-apoptotic mechanism of Bcl-B

scientific article published on November 2003

ChlaDub1 of Chlamydia trachomatis suppresses NF-kappaB activation and inhibits IkappaBalpha ubiquitination and degradation

scientific journal article

Cleavage targets and the D-arginine-based inhibitors of the West Nile virus NS3 processing proteinase

scientific article (publication date: 15 January 2006)

Cloning and characterization of glucose transporter 11, a novel sugar transporter that is alternatively spliced in various tissues

scientific article

Clustering of highly homologous sequences to reduce the size of large protein databases

scientific article

Cofactor-induced reversible folding of Flavodoxin-4 from Lactobacillus acidophilus

scientific article

Combination of multiple alignment analysis and surface mapping paves a way for a detailed pathway reconstruction--the case of VHL (von Hippel-Lindau) protein and angiogenesis regulatory pathway

scientific article published on 6 February 2004

Comparative analysis of apoptosis and inflammation genes of mice and humans

scientific article

Comparative analysis of protein domain organization

scientific article published on March 2004

Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution

scientific article published in November 2006

Comparison of algorithms for the detection of cancer drivers at subgene resolution

scientific article published on 17 July 2017

Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis

scientific article published on 19 April 2020

Comparison of sequence profiles. Strategies for structural predictions using sequence information

scientific article published on February 2000

Comprehensive Characterization of Cancer Driver Genes and Mutations

scientific article published in April 2018

Comprehensive Characterization of Cancer Driver Genes and Mutations

article

Computational protein function prediction: are we making progress?

scientific article published on October 2007

ConSole: using modularity of contact maps to locate solenoid domains in protein structures

scientific article

Conformational changes associated with the binding of zinc acetate at the putative active site of Xc TcmJ, a cupin from Xanthomonas campestris pv. campestris

scientific article

Conformational role of His-12 in C-peptide of ribonuclease A

scientific article published on 01 August 1988

Connecting the protein structure universe by using sparse recurring fragments.

scientific article

Conservation of residue interactions in a family of Ca-binding proteins

article

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

scientific article

Convergent evolution as a mechanism for pathogenic adaptation

scientific article

Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence

scientific article published on 29 May 2020

Correction: Structure of an MmyB-Like Regulator from C. aurantiacus, Member of a New Transcription Factor Family Linked to Antibiotic Metabolism in Actinomycetes

scientific article

Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome

scientific article

Crystal Structure of Histidine Phosphotransfer Protein ShpA, an Essential Regulator of Stalk Biogenesis in Caulobacter crescentus

scientific article

Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that May Discriminate Substrates During DNA Repair

scientific article

Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution

scientific article

Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site

scientific article

Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolution

scientific article

Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution

article

Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 angstroms resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate

scientific article

Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 angstroms resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases

scientific article

Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2

scientific article published on 3 March 2020

Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2

scientific article published on 17 April 2020

Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution

scientific article published in August 2004

Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 A resolution reveals a new fold

scientific article

Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function

scientific article published in July 2007

Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold

scientific article published in June 2006

Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution

scientific article

Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 Å resolution reveals a new fold

article

Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold

scientific article

Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 Å resolution reveals a new fold

article

Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution

scientific article published in July 2004

Crystal structure of a member of a novel family of dioxygenases (PF10014) reveals a conserved cupin fold and active site

scientific article

Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity

scientific article

Crystal structure of a methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.9 A resolution

scientific article

Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution

scientific article

Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution

scientific article published in August 2004

Crystal structure of a novel archaeal AAA+ ATPase SSO1545 fromSulfolobus solfataricus

scientific article

Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution

scientific article

Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-A resolution

scientific article published in May 2004

Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution

scientific article

Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution

scientific article published in March 2004

Crystal structure of a putative glutamine amido transferase (TM1158) from Thermotoga maritima at 1.7 A resolution

scientific article published in March 2004

Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold

scientific article

Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 A resolution

scientific journal article

Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family

scientific article

Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution

scientific article

Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution

article

Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution

scientific article

Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 A resolution

scientific article

Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 A resolution.

scientific article published in May 2004

Crystal structure of a zinc-containing glycerol dehydrogenase (TM0423) from Thermotoga maritima at 1.5 A resolution

scientific article

Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution

scientific article

Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution

scientific article

Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution

scientific article

Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution

scientific article published in March 2004

Crystal structure of an ORFan protein (TM1622) fromThermotoga maritimaat 1.75 Å resolution reveals a fold similar to the Ran-binding protein Mog1p

article

Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution

scientific article published in June 2004

Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor

scientific article published in March 2005

Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution

scientific article

Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution

scientific article

Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution

scientific article published in May 2004

Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 Å resolution reveals a new fold

article

Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution

scientific article

Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-A resolution reveals a new fold

scientific article published in August 2004

Crystal structure of gamma-glutamyl phosphate reductase (TM0293) from Thermotoga maritima at 2.0 A resolution

scientific article

Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution

scientific article

Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution

scientific article published in October 2006

Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution

scientific article

Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution

article

Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 Å resolution

scientific article

Crystal structure of the actin binding domain of the cyclase-associated protein

scientific article

Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 A resolution reveals a new fold

scientific article published in November 2005

Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution

scientific article

Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution

scientific article

Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 A resolution reveals a new fold

scientific article

Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold

scientific article

Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake

scientific article

Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif

scientific article

CutDB: a proteolytic event database

scientific article (publication date: 2007)

Cysteine regulation of protein function--as exemplified by NMDA-receptor modulation.

scientific article

Data bases in biochemistry--applications to analysis and prediction of protein properties and function

scientific article

Database searching by flexible protein structure alignment.

scientific article

De novo and inverse folding predictions of protein structure and dynamics

scientific article

Defining the risk of SARS-CoV-2 variants on immune protection

scientific article published on 31 March 2022

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

scientific article published on March 1997

Detection of a SARS-CoV-2 variant of concern in South Africa

scientific article

Difference contact maps: From what to why in the analysis of the conformational flexibility of proteins

scientific article published on 12 March 2020

Discovering new genes with advanced homology detection

article

Divergent evolution of protein conformational dynamics in dihydrofolate reductase

scientific article

Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization

scientific article

Domain architecture evolution of pattern-recognition receptors

scientific article

Draft Genome Sequences of Two Vibrio parahaemolyticus Strains Associated with Gastroenteritis after Raw Seafood Ingestion in Colorado.

scientific article published on 18 January 2018

Drosophila pro-apoptotic Bcl-2/Bax homologue reveals evolutionary conservation of cell death mechanisms

scientific article published on September 2000

Dynamics of coregulator-induced conformational perturbations in androgen receptor ligand binding domain

article

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

scientific article

Evolution of the animal apoptosis network

scientific article published on March 2013

Evolution of the protein domain repertoire of eukaryotes reveals strong functional patterns.

scientific article

Evolutionarily conserved cytoprotection provided by Bax Inhibitor-1 homologs from animals, plants, and yeast

scientific article

Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families

scientific article

Exploration of uncharted regions of the protein universe

scientific article published in September 2009

FATCAT 2.0: towards a better understanding of the structural diversity of proteins

scientific article published on 29 May 2020

FATCAT: a web server for flexible structure comparison and structure similarity searching

scientific article

FFAS server: novel features and applications

scientific article

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking

scientific article published on 15 October 2013

FFAS03: a server for profile--profile sequence alignments

scientific article

Flexible Structural Neighborhood--a database of protein structural similarities and alignments

scientific article

Flexible algorithm for direct multiple alignment of protein structures and sequences

scientific article published in December 1994

Flexible structure alignment by chaining aligned fragment pairs allowing twists

scientific article (publication date: October 2003)

Fold and function predictions for Mycoplasma genitalium proteins

scientific article

Fold prediction by a hierarchy of sequence, threading, and modeling methods

scientific article published on June 1998

Fold predictions for bacterial genomes.

scientific article

Fold recognition methods.

scientific article

Fragnostic: walking through protein structure space

scientific article

From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions

scientific article published on May 1999

From fold to function predictions: an apoptosis regulator protein BID.

scientific article

From independent modules to molten globules: observations on the nature of protein folding intermediates

scientific article

Function driven protein evolution. A possible proto-protein for the RNA-binding proteins ⬇️

scientific article published on January 1, 1998

Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family

scientific article published on January 1998

Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity

scientific article published in October 1998

Functional differentiation of proteins: implications for structural genomics.

scientific article

Functional insights from structural predictions: analysis of the Escherichia coli genome.

scientific article

Genome pool strategy for structural coverage of protein families

scientific article

Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure.

scientific article

HEPN: a common domain in bacterial drug resistance and human neurodegenerative proteins

scientific article

Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family

scientific article published on September 2003

Homotypic secretory vesicle fusion induced by the protein tyrosine phosphatase MEG2 depends on polyphosphoinositides in T cells

scientific article

Identification and Functional Characterization of the BAG Protein Family inArabidopsis thaliana

scientific article published in Journal of Biological Chemistry

Identification and characterization of DEDD2, a death effector domain-containing protein

scientific article

Identification and characterization of DUSP27, a novel dual-specific protein phosphatase

scientific article

Identification and characterization of a novel bacterial virulence factor that shares homology with mammalian Toll/interleukin-1 receptor family proteins

scientific article

Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins.

scientific article

Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA

scientific article

Improving the chances of successful protein structure determination with a random forest classifier

scientific article

In search for more accurate alignments in the twilight zone

scientific article

In search of the ideal protein sequence

scientific article

Inhibition of T cell antigen receptor signaling by VHR-related MKPX (VHX), a new dual specificity phosphatase related to VH1 related (VHR).

scientific article

Insights into Substrate Specificity of Geranylgeranyl Reductases Revealed by the Structure of Digeranylgeranylglycerophospholipid Reductase, an Essential Enzyme in the Biosynthesis of Archaeal Membrane Lipids

scientific article

Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains

scientific article published on 15 September 2015

Integrated web service for improving alignment quality based on segments comparison

scientific article

Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering

scientific article

Ion channel activity of the BH3 only Bcl-2 family member, BID.

scientific article published on July 1999

JAFA: a protein function annotation meta-server

scientific article published on July 2006

Knowledge-based potentials for protein folding: what can we learn from known protein structures?

scientific article

LUD, a new protein domain associated with lactate utilization

scientific article

MORPH-PRO: a novel algorithm and web server for protein morphing

scientific article

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

scientific article published on 18 December 2017

Metagenomics and the protein universe

scientific article

Microbial function and genital inflammation in young South African women at high risk of HIV infection

scientific article published on 21 November 2020

Mitochondrial fission in apoptosis, neurodegeneration and aging

scientific article published on December 2003

ModFlex: Towards Function Focused Protein Modeling

scientific article published on 23 January 2021

Modeling and analyzing three-dimensional structures of human disease proteins

article

Molecular characterization of novel pyridoxal-5′-phosphate-dependent enzymes from the human microbiome

scientific article

Molecular modeling of phosphorylation sites in proteins using a database of local structure segments

scientific article published on 11 August 2005

Multiple flexible structure alignment using partial order graphs.

scientific article

Multiple model approach--dealing with alignment ambiguities in protein modeling

scientific article published in January 1997

Mutation Drivers of Immunological Responses to Cancer

scientific article published on 11 July 2016

NERD: a DNA processing-related domain present in the anthrax virulence plasmid, pXO1.

scientific article published in March 2004

NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia

scientific article

Neutralizing antibody affords comparable protection against vaginal and rectal simian/human immunodeficiency virus challenge in macaques.

scientific article published on June 2016

New avenues in protein function prediction

scientific article published in June 2006

Non-proteolytic, receptor/ligand interactions associate cellular membrane type-1 matrix metalloproteinase with the complement component C1q.

scientific article published on 16 September 2004

Novel SARS unique AdoMet-dependent methyltransferase

scientific article published on 16 October 2006

Novel genes dramatically alter regulatory network topology in amphioxus

scientific article published on 04 August 2008

Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination

scientific article published on 06 July 2016

On the interactions of charged side chains with the α-helix backbone

scientific article published on 01 August 1988

Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding

scientific article

Outcome of a workshop on applications of protein models in biomedical research

scientific article (publication date: 13 February 2009)

Outcome of a workshop on archiving structural models of biological macromolecules

scientific article

PAAD - a new protein domain associated with apoptosis, cancer and autoimmune diseases.

scientific article

PDBFlex: exploring flexibility in protein structures

scientific article

PMAP: databases for analyzing proteolytic events and pathways

scientific article

POSA: a user-driven, interactive multiple protein structure alignment server

scientific article

PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB

scientific article

PSI-2: structural genomics to cover protein domain family space.

scientific article

Phylogenomic analysis of glycogen branching and debranching enzymatic duo

scientific article

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks

scientific article

Practical lessons from protein structure prediction

scientific article

Pre-calculated protein structure alignments at the RCSB PDB website

scientific article published in December 2010

Probing metagenomics by rapid cluster analysis of very large datasets

scientific article

Protael: protein data visualization library for the web.

scientific article

Protein structure prediction in biology and medicine

scientific article published in January 2000

Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage

scientific article published on 19 October 2020

Protein tyrosine phosphatases in the human genome

scientific article

PubServer: literature searches by homology

scientific article

Putative type IV secretion genes in Bacillus anthracis

article

Regularities in interaction patterns of globular proteins

scientific article

Representing and comparing protein structures as paths in three-dimensional space.

scientific article

Retraction: Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50, William C. Hwang, Qingping Xu, Bainan Wu, Adam Godzik

scientific article

Retraction: Site‐specific recombination of nitrogen‐fixation genes in cyanobacteria by XisF–XisH–XisI complex: Structures and models, William C. Hwang, James W. Golden, Jaime Pascual, Dong Xu, Anton Cheltsov, Adam Godzik

scientific article

Revealing aperiodic aspects of solenoid proteins from sequence information

scientific article published on 9 June 2016

S-nitrosylation of Drp1 links excessive mitochondrial fission to neuronal injury in neurodegeneration

scientific article

S-nitrosylation of Drp1 mediates beta-amyloid-related mitochondrial fission and neuronal injury

scientific article

S-nitrosylation-mediated redox transcriptional switch modulates neurogenesis and neuronal cell death

scientific article published on 4 July 2014

SURF'S UP! - protein classification by surface comparisons

scientific article published in January 2007

Salmonella secreted factor L deubiquitinase of Salmonella typhimurium inhibits NF-kappaB, suppresses IkappaBalpha ubiquitination and modulates innate immune responses

scientific article published in April 2008

Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology.

scientific article published in December 2000

Search for a new description of protein topology and local structure.

scientific article

Secondary structure prediction using segment similarity

scientific article published on October 1997

Sensitive sequence comparison as protein function predictor

scientific article published in January 2000

Sensor domains encoded in Bacillus anthracis virulence plasmids prevent sporulation by hijacking a sporulation sensor histidine kinase

scientific article

Sequence clustering strategies improve remote homology recognitions while reducing search times

scientific article published on 01 August 2002

Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination

scientific article published on December 1992

Sequence-structure specificity--how does an inverse folding approach work?

scientific article

Shotgun metaproteomics of the human distal gut microbiota

article

Similarities and differences between nonhomologous proteins with similar folds: evaluation of threading strategies

scientific article published in January 1997

Simulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins

scientific article

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

scientific article (publication date: 2011)

Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites

scientific article

Structural Basis of Murein Peptide Specificity of a γ-D-Glutamyl-L-Diamino Acid Endopeptidase

scientific article

Structural Diversity in a Family of Homologous Proteins

Structural Insights into Inhibition of Bacillus anthracis Sporulation by a Novel Class of Non-heme Globin Sensor Domains

scientific article

Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications

scientific article

Structural and Functional Analysis of the Globular Head Domain of p115 Provides Insight into Membrane Tethering

scientific article

Structural and Sequence Analysis of Imelysin-Like Proteins Implicated in Bacterial Iron Uptake

scientific article

Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes

scientific article

Structural determinants of limited proteolysis

scientific article

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase

scientific article

Structural genomics is the largest contributor of novel structural leverage

scientific article published on 05 February 2009

Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline

scientific article

Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability

scientific article published in June 2005

Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli

scientific article

Structural systems biology: from bacterial to cancer networks

Structure and Function of a Novel LD-Carboxypeptidase A Involved in Peptidoglycan Recycling

scientific article

Structure and Function of the DUF2233 Domain in Bacteria and in the Human Mannose 6-Phosphate Uncovering Enzyme

scientific article

Structure and Function of the First Full-Length Murein Peptide Ligase (Mpl) Cell Wall Recycling Protein

scientific article

Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis

scientific article

Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

scientific article

Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules

scientific article

Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism

scientific article

Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism

scientific article

Structure of a Novel Winged-Helix Like Domain from Human NFRKB Protein

scientific article

Structure of a Virulence Regulatory Factor CvfB Reveals a Novel Winged Helix RNA Binding Module

scientific article

Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron

scientific article

Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15

scientific article

Structure of a tryptophanyl-tRNA synthetase containing an iron–sulfur cluster

scientific article

Structure of an MmyB-Like Regulator from C. aurantiacus, Member of a New Transcription Factor Family Linked to Antibiotic Metabolism in Actinomycetes

scientific article

Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution

scientific article

Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment

scientific article published on 17 December 2019

Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation

scientific article

Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism

scientific article

Structure of the pilus assembly protein TadZ from Eubacterium rectale: implications for polar localization

scientific article

Structure of the γ- D -glutamyl- L -diamino acid endopeptidase YkfC from Bacillus cereus in complex with L -Ala-γ- D -Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases

scientific article

Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase

scientific article

Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells

scientific article

Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family

scientific article

Structures of a Bifunctional Cell Wall Hydrolase CwlT Containing a Novel Bacterial Lysozyme and an NlpC/P60 dl-Endopeptidase

scientific article

Structures of single-layer β-sheet proteins evolved from β-hairpin repeats

scientific article published on 02 August 2019

Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism

scientific article

Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction

scientific article

Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger

scientific article

Subunit-specific roles of glycine-binding domains in activation of NR1/NR3 N-methyl-D-aspartate receptors

scientific article

Support-vector-machine classification of linear functional motifs in proteins.

scientific article

Surface Map Comparison: Studying Function Diversity of Homologous Proteins

article by Krzysztof Pawłowski & Adam Godzik published June 2001 in Journal of Molecular Biology

Surprising complexity of the ancestral apoptosis network

scientific article

TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog

scientific article

TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model.

scientific article

TOPSAN: a collaborative annotation environment for structural genomics

scientific article

TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures

scientific article

TUCAN, an antiapoptotic caspase-associated recruitment domain family protein overexpressed in cancer.

scientific article published on 14 June 2001

The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability

scientific article

The 2006 Automated Function Prediction Meeting

scientific article

The Aspergillus nidulans cysA gene encodes a novel type of serine O-acetyltransferase which is homologous to homoserine O-acetyltransferases

scientific article published on October 2000

The Drosophila tumor necrosis factor receptor-associated factor-1 (DTRAF1) interacts with Pelle and regulates NFkappaB activity.

scientific article

The FGGY carbohydrate kinase family: insights into the evolution of functional specificities

scientific article

The Functional Impact of Alternative Splicing in Cancer

scientific article published in August 2017

The Helicobacter pylori genome: from sequence analysis to structural and functional predictions

scientific article published on July 1999

The JCSG MR pipeline: optimized alignments, multiple models and parallel searches

scientific article published on 5 December 2007

The JCSG high-throughput structural biology pipeline

scientific article (publication date: October 2010)

The Monte Carlo simulation of pearl chain formation

scientific article published in January 1987

The NLR gene family: a standard nomenclature

scientific article

The PAAD/PYRIN-only protein POP1/ASC2 is a modulator of ASC-mediated nuclear-factor-kappa B and pro-caspase-1 regulation

scientific article

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families

scientific article published in March 2007

The Structure of Mlc Titration Factor A (MtfA/YeeI) Reveals a Prototypical Zinc Metallopeptidase Related to Anthrax Lethal Factor

scientific article

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

scientific article

The apoptosis database

scientific article

The challenge of protein structure determination--lessons from structural genomics.

scientific article

The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu

scientific article

The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine

scientific article published on 20 April 2020

The domains of apoptosis: a genomics perspective

scientific article

The functional impact of alternative splicing in cancer

The importance of alignment accuracy for molecular replacement.

scientific article published on 22 June 2004

The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins

scientific article published on 10 August 2020

The interplay of fold recognition and experimental structure determination in structural genomics

scientific article published on June 2004

The minimal essential core of a cysteine-based protein-tyrosine phosphatase revealed by a novel 16-kDa VH1-like phosphatase, VHZ.

scientific article

The retinitis pigmentosa GTPase regulator (RPGR)- interacting protein: subserving RPGR function and participating in disk morphogenesis

scientific journal article

The signal for signaling, found

scientific article

The status of structural genomics defined through the analysis of current targets and structures

scientific article published on January 2004

The structural alignment between two proteins: is there a unique answer?

scientific article

The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

scientific article

The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes

scientific article

The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator

scientific article

The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae , reveals an OB-fold

scientific article

The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

scientific article

The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism

scientific article

The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

scientific article

This Déjà Vu Feeling—Analysis of Multidomain Protein Evolution in Eukaryotic Genomes ⬇️

scientific article published on November 15, 2012

Three-dimensional structural view of the central metabolic network of Thermotoga maritima

scientific article

Tolerating some redundancy significantly speeds up clustering of large protein databases

scientific article published in January 2002

Topology fingerprint approach to the inverse protein folding problem

scientific article

Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila

scientific article

Tyrosine phosphorylation of VHR phosphatase by ZAP-70

scientific article

UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex

scientific article published on 24 March 2016

Understanding diversity of human innate immunity receptors: analysis of surface features of leucine-rich repeat domains in NLRs and TLRs

scientific article

Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era

scientific article published on 01 April 2020

Using an alignment of fragment strings for comparing protein structures.

scientific article

VISSA: a program to visualize structural features from structure sequence alignment

scientific article published on 24 January 2006

XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators

scientific article

XtalPred: a web server for prediction of protein crystallizability

scientific article published in 2007

bNAber: database of broadly neutralizing HIV antibodies

scientific article

e-Driver: a novel method to identify protein regions driving cancer

scientific article published on 26 July 2014

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