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List of works by Andrej Šali

2007 annual progress report synopsis of the Center for Structures of Membrane Proteins.

scientific article

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

scientific article published on 18 August 2017

A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen-Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions

scientific article

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

scientific article published on 30 April 2020

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing ⬇️

journal article from 'bioRxiv' published in 2020

A composite score for predicting errors in protein structure models

scientific article

A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae

scientific article

A kernel for open source drug discovery in tropical diseases

scientific article

A kernel for the Tropical Disease Initiative

scientific article

A method for integrative structure determination of protein-protein complexes

scientific article

A phosphotyrosine switch regulates organic cation transporters ⬇️

scientific article published on 16 March 2016

A structural perspective on protein-protein interactions.

scientific article

A survey of integral alpha-helical membrane proteins

scientific article published on 17 September 2009

A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis

scientific article

Accurate SAXS profile computation and its assessment by contrast variation experiments

scientific article published on August 2013

Alignment of multiple protein structures based on sequence and structure features.

scientific article

Alignment of protein sequences by their profiles

scientific article

All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins

scientific article

An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome

scientific article published on 03 August 2009

Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer

scientific article published on 16 October 2015

Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images ⬇️

scientific article published on October 29, 2012

Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures

scientific article

Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking

scientific article published on 2 January 2013

Atomic structure of the nuclear pore complex targeting domain of a nup116 homologue from the yeast, Candida glabrata

scientific article

Biochemical characterization and structural modeling of human cathepsin E variant 2 in comparison to the wild-type protein

scientific article

Biochemistry. Integrative structural biology

scientific article published on February 2013

Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase, ⬇️

scientific article published on February 4, 2011

Characterization of protein hubs by inferring interacting motifs from protein interactions

scientific article

Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios.

scientific article

Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23

scientific article (publication date: 23 November 2016)

Combining electron microscopy and comparative protein structure modeling.

scientific article published in October 2005

Comparative Protein Structure Modeling Using MODELLER

scientific article

Comparative Protein Structure Modeling Using MODELLER.

scientific article published on 20 June 2016

Comparative Protein Structure Modeling Using MODELLER.

scientific article published in November 2016

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

scientific article published on 15 October 2020

Comparative protein structure modeling by iterative alignment, model building and model assessment

scientific article

Comparison of human solute carriers

scientific article

Components of coated vesicles and nuclear pore complexes share a common molecular architecture

scientific article

Comprehensive Molecular Structure of the Eukaryotic Ribosome

scientific article

Comprehensive search for cysteine cathepsins in the human genome

scientific article

Computational Discovery and Experimental Validation of Inhibitors of the Human Intestinal Transporter OATP2B1.

scientific article

Consequences of domain insertion on sequence-structure divergence in a superfold

scientific article published on 19 August 2013

Coordinating the impact of structural genomics on the human α-helical transmembrane proteome

scientific article

Correction: Components of Coated Vesicles and Nuclear Pore Complexes Share a Common Molecular Architecture

scientific article

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

scientific article published on 4 February 2016

Crystal structure of a eukaryotic phosphate transporter

scientific article

Crystallographic Conformers of Actin in a Biologically Active Bundle of Filaments

scientific article

Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ.

scientific article

DBAli tools: mining the protein structure space

scientific article

Deamination of 6-Aminodeoxyfutalosine in Menaquinone Biosynthesis by Distantly Related Enzymes

scientific article

Detecting remotely related proteins by their interactions and sequence similarity

scientific article

Detection of homologous proteins by an intermediate sequence search

scientific article published in January 2004

Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis

scientific article

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map ⬇️

scientific article published on November 15, 2010

Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data

scientific article

Determining the architectures of macromolecular assemblies

scientific article

Discovery of Competitive and Noncompetitive Ligands of the Organic Cation Transporter 1 (OCT1; SLC22A1).

scientific article

Discovery of a Cytokinin Deaminase ⬇️

scientific article published on August 12, 2011

Discovery of potent, selective multidrug and toxin extrusion transporter 1 (MATE1, SLC47A1) inhibitors through prescription drug profiling and computational modeling

scientific article

Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain

scientific article published on 29 April 2022

EVA: Evaluation of protein structure prediction servers.

scientific article

Editorial overview: Biophysical and molecular biological methods

scientific article published on 28 November 2016

Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone

scientific article published on 12 April 2014

Enzymatic deamination of the epigenetic base N-6-methyladenine

scientific article published on 28 January 2011

Erratum: Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex.

erratum

Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor

scientific article published on 13 June 2009

Evolution and physics in comparative protein structure modeling.

scientific article

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies

scientific article

Evolutionary constraints on structural similarity in orthologs and paralogs

scientific article published on June 2009

Facile backbone structure determination of human membrane proteins by NMR spectroscopy

scientific article

Finding cures for tropical diseases: is open source an answer?

scientific article

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

scientific article published on 05 May 2016

FoXS: a web server for rapid computation and fitting of SAXS profiles

scientific article

Fold assessment for comparative protein structure modeling.

scientific article

From words to literature in structural proteomics

scientific article

Function of human Rh based on structure of RhCG at 2.1 A

scientific article

Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains

scientific article

Functional impact of missense variants in BRCA1 predicted by supervised learning

scientific article

Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term

scientific article published on 14 December 2006

Genetic interaction mapping informs integrative structure determination of protein complexes

scientific article published on 01 December 2020

Genomic-scale prioritization of drug targets: the TDR Targets database

scientific article

Global Identification and Characterization of Both O-GlcNAcylation and Phosphorylation at the Murine Synapse ⬇️

scientific article published on May 29, 2012

Global landscape of HIV-human protein complexes

scientific article

Global motions of the nuclear pore complex: insights from elastic network models

scientific article

Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini

scientific article

Glutamine Side Chain 13C═18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly

scientific article published on 24 April 2019

Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions

scientific article published on 20 July 2016

High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach

scientific article

High-resolution network biology: connecting sequence with function

scientific article

High-throughput computational and experimental techniques in structural genomics

scientific article published on October 2004

Host pathogen protein interactions predicted by comparative modeling

scientific article

How well can the accuracy of comparative protein structure models be predicted?

scientific article

Human Concentrative Nucleoside Transporter 3 (hCNT3, SLC28A3) Forms a Cyclic Homotrimer.

scientific article

Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates

scientific article published in 2024

Immunoproteasome functions explained by divergence in cleavage specificity and regulation.

scientific article published on 28 November 2017

Impact of mutations on the allosteric conformational equilibrium

scientific article published on 7 December 2012

Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone

scientific article published on 11 March 2019

Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly

scientific article published on 20 February 2009

Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

scientific article published on 12 October 2016

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters ⬇️

scientific article published in July 2014

Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy

scientific article

Integrating diverse data for structure determination of macromolecular assemblies

scientific article

Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies

scientific article

Integrative structural modeling with small angle X-ray scattering profiles ⬇️

scientific article published on July 16, 2012

Integrative structure modeling of macromolecular assemblies from proteomics data

scientific article

Integrative structure modeling with the Integrative Modeling Platform

scientific article published on 28 September 2017

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

scientific article

Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy.

scientific article

LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures.

scientific article

Ligand discovery from a dopamine D3 receptor homology model and crystal structure

scientific article

Limits of ligand selectivity from docking to models: in silico screening for A(1) adenosine receptor antagonists

scientific article

Lineage-specific proteins essential for endocytosis in trypanosomes

scientific article

Localization of binding sites in protein structures by optimization of a composite scoring function

scientific article

Localization of protein-binding sites within families of proteins

scientific article published on 4 August 2005

MODBASE, a database of annotated comparative protein structure models, and associated resources.

scientific article

MODBASE: a database of annotated comparative protein structure models and associated resources

scientific article

Macromolecular Assembly Structures by Comparative Modeling and Electron Microscopy ⬇️

scientific article published on January 1, 2012

Macromolecular docking restrained by a small angle X-ray scattering profile

scientific article

Mapping polymerization and allostery of hemoglobin S using point mutations

scientific article published on 09 September 2013

Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT

scientific article published on 8 June 2008

Minimalist representations and the importance of nearest neighbor effects in protein folding simulations

scientific article

ModBase, a database of annotated comparative protein structure models and associated resources.

scientific article

ModBase, a database of annotated comparative protein structure models, and associated resources

scientific article

ModLoop: automated modeling of loops in protein structures

scientific article (publication date: 12 December 2003)

Modeling mutations in protein structures

scientific article published on September 2007

Modeling of proteins and their assemblies with the Integrative Modeling Platform

scientific article published in January 2014

Modeling of proteins and their assemblies with the integrative modeling platform

scientific article published in January 2011

Modeller: generation and refinement of homology-based protein structure models

scientific article (publication date: 2003)

Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.

scientific article published on 2 February 2017

Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling

scientific article

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

scientific article

Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex

scientific article

Molecular architecture of the yeast Mediator complex

scientific article

Molecular docking screens using comparative models of proteins

scientific article

Molecular modeling and ligand docking for solute carrier (SLC) transporters

scientific article

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map ⬇️

scientific article published on July 1, 2011

Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.

scientific article published on May 2008

NIH workshop on structural proteomics of biological complexes

scientific article published in September 2003

New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative.

scientific article

Optimized atomic statistical potentials: assessment of protein interfaces and loops

scientific article published on 27 September 2013

Optimizing model representation for integrative structure determination of macromolecular assemblies

scientific article published on 26 December 2018

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

scientific article (publication date: 13 February 2009)

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

scientific article published on 18 June 2015

Outcome of the first electron microscopy validation task force meeting

scientific article (publication date: 8 February 2012)

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

scientific article

PIBASE: a comprehensive database of structurally defined protein interfaces

scientific article published on 18 January 2005

PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network

scientific article published in March 2006

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.

scientific article

Prediction of enzymatic pathways by integrative pathway mapping.

scientific article

Prediction of enzyme function by combining sequence similarity and protein interactions

scientific article

Prediction of protease substrates using sequence and structure features

scientific article

Prediction of substrates for glutathione transferases by covalent docking

scientific article

Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering

scientific article

Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis

scientific article

Protease accessibility laddering: a proteomic tool for probing protein structure.

scientific article

Protein complex compositions predicted by structural similarity

scientific article published on 31 May 2006

Protein interactions and disease phenotypes in the ABC transporter superfamily.

scientific article

Protein production and purification

scientific article

Protein structure fitting and refinement guided by cryo-EM density

scientific article

Protein structure modeling with MODELLER.

scientific article

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies ⬇️

scientific article published on January 17, 2012

RasGRP4, a new mast cell-restricted Ras guanine nucleotide-releasing protein with calcium- and diacylglycerol-binding motifs. Identification of defective variants of this signaling protein in asthma, mastocytosis, and mast cell leukemia patients and

scientific article

Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination

scientific article

Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages

scientific article

Recovering a representative conformational ensemble from underdetermined macromolecular structural data

scientific article

Refinement of protein structures by iterative comparative modeling and CryoEM density fitting

scientific article

Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones

scientific article published on June 2017

Regulatory elements within the prodomain of Falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum

scientific article

Reliability of assessment of protein structure prediction methods.

scientific article

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

scientific article

Ring closure activates yeast γTuRC for species-specific microtubule nucleation

scientific article

Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin

scientific article

SALIGN: a web server for alignment of multiple protein sequences and structures

scientific article

SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes

scientific article published on 14 December 2013

Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.

scientific article published on 9 March 2015

Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening

scientific article

Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils

scientific article

Simple fold composition and modular architecture of the nuclear pore complex

scholarly article

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

scientific article published on 18 April 2016

Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking

scientific article

Statistical potential for modeling and ranking of protein-ligand interactions

scientific article published on 21 November 2011

Statistical potentials for fold assessment.

scientific article

Stereochemical criteria for prediction of the effects of proline mutations on protein stability

scientific article

Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data

scientific article

Structural basis for alternating access of a eukaryotic calcium/proton exchanger

scientific article

Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

scientific article

Structural characterization of assemblies from overall shape and subcomplex compositions

scientific article published in March 2005

Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy.

scientific article

Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling

scientific article published on 07 February 2020

Structural genomics of protein phosphatases

scientific article

Structural genomics: A pipeline for providing structures for the biologist

scientific article

Structural modeling of protein interactions by analogy: application to PSD-95

scientific article

Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 Å resolution

scientific article

Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex

scientific article

Structure of the Mammalian 80S Ribosome at 8.7 Å Resolution

scientific article

Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure

scientific article published on 8 March 2016

Structure, Dynamics, Evolution, and Function of a Major Scaffold Component in the Nuclear Pore Complex

scientific article

Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET.

scientific article

Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1

scientific article published on 18 March 2013

Structure-based model of allostery predicts coupling between distant sites ⬇️

scientific article published on March 8, 2012

Structure-guided discovery of new deaminase enzymes

scientific journal article

Structures of the autoproteolytic domain from theSaccharomyces cerevisiaenuclear pore complex component, Nup145

scientific article

Study of the structural dynamics of the E coli 70S ribosome using real-space refinement

scientific article

Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel

scientific article

Target prediction for an open access set of compounds active against Mycobacterium tuberculosis

scientific article (publication date: 2013)

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

scientific article published on 14 February 2009

Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break.

scientific article

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.

scientific article

The C-type lectin fold as an evolutionary solution for massive sequence variation

scientific article

The Enzyme Function Initiative

scientific article

The YΦ motif defines the structure-activity relationships of human 20S proteasome activators

scientific article published on 09 March 2022

The molecular architecture of the nuclear pore complex

scientific article

The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

scientific article

The molecular sociology of the cell

scientific article published on December 2007

The overlap of small molecule and protein binding sites within families of protein structures

scientific article

The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress

scientific article published on 15 August 2017

The structural dynamics of macromolecular processes

scientific article published on 14 February 2009

The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family

scientific article

The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons ⬇️

scientific article published on June 1, 2003

Tools for comparative protein structure modeling and analysis

scientific article

Topological models of heteromeric protein assemblies from mass spectrometry: application to the yeast eIF3:eIF5 complex

scientific article

Toward an integrated structural model of the 26S proteasome

scientific article

UCSF Chimera, MODELLER, and IMP: an integrated modeling system

scientific article

Uncertainty in integrative structural modeling

scientific article

Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22

scientific article

Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies

scientific article published in December 2002

Variable gap penalty for protein sequence-structure alignment

scientific article published on 19 January 2006

Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection ⬇️

scientific article published on December 21, 2011

Virtual Ligand Screening Against Comparative Protein Structure Models ⬇️

scientific article published on January 1, 2012

Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography

scientific article published on 09 December 2020

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