Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling

Mass spectrometry–based molecular mapping of native FXIIIa cross-links in insoluble fibrin clots

(2019) Lauren R. Schmitt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Hereditary Fibrinogen Aα-Chain Amyloidosis in Asia: Clinical and Molecular Characteristics

(2018) Masahide Yazaki et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Atomic Structural Models of Fibrin Oligomers

(2018) Artem Zhmurov et al.   STRUCTURE

Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue

(2018) Juan D. Chavez et al.   Cell Systems

Cross-ID: Analysis and Visualization of Complex XL–MS-Driven Protein Interaction Networks

(2018) Sebastiaan C. de Graaf et al.   JOURNAL OF PROTEOME RESEARCH

Efficient and robust proteome-wide approaches for cross-linking mass spectrometry

(2018) Oleg Klykov et al.   Nature Protocols

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Capturing protein communities by structural proteomics in a thermophilic eukaryote

(2017) Panagiotis L Kastritis et al.   Molecular Systems Biology

ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly

(2017) Yan Wang et al.   NUCLEIC ACIDS RESEARCH

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Strong Binding of Platelet Integrin αIIbβ3 to Fibrin Clots: Potential Target to Destabilize Thrombi

(2017) Peter Höök et al.   Scientific Reports

Accounting for pairwise distance restraints in FFT-based protein–protein docking

(2016) Bing Xia et al.   BIOINFORMATICS

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

(2016) Haim Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Cross-linking reveals laminin coiled-coil architecture

(2016) Gad Armony et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis of Interfacial Flexibility in Fibrin Oligomers

(2016) Artem Zhmurov et al.   STRUCTURE

Plasma Proteome Profiling to Assess Human Health and Disease

(2016) Philipp E. Geyer et al.   Cell Systems

HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling: Fig. 1.

(2015) Jinchao Yu et al.   BIOINFORMATICS

DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes: Fig. 1.

(2015) G.C.P. van Zundert et al.   BIOINFORMATICS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption

(2015) Stephan Köhler et al.   PLoS Computational Biology

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

On the Mechanism of αC Polymer Formation in Fibrin

(2012) Galina Tsurupa et al.   BIOCHEMISTRY

Improved model quality assessment using ProQ2

(2012) Arjun Ray et al.   BMC BIOINFORMATICS

Evidence that fibrinogen γ′ directly interferes with protofibril growth: implications for fibrin structure and clot stiffness

(2012) P. ALLAN et al.   JOURNAL OF THROMBOSIS AND HAEMOSTASIS

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

Identification of Fibrin Clot-Bound Plasma Proteins

(2012) Simone Talens et al.   PLoS One

Visualization and identification of the structures formed during early stages of fibrin polymerization

(2011) I. N. Chernysh et al.   BLOOD

Mechanobiology of Platelets: Techniques to Study the Role of Fluid Flow and Platelet Retraction Forces at the Micro- and Nano-Scale

(2011) Shirin Feghhi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK

(2011) Sjoerd J. de Vries et al.   PLoS One

High-Resolution Visualization of Fibrinogen Molecules and Fibrin Fibers with Atomic Force Microscopy

(2010) Ivan S. Yermolenko et al.   BIOMACROMOLECULES

Thrombin Flux and Wall Shear Rate Regulate Fibrin Fiber Deposition State during Polymerization under Flow

(2010) K.B. Neeves et al.   BIOPHYSICAL JOURNAL

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Toward an understanding of fibrin branching structure

(2010) Aaron L. Fogelson et al.   PHYSICAL REVIEW E

Crystal Structure of Human Fibrinogen

(2009) Justin M. Kollman et al.   BIOCHEMISTRY

High prevalence of dysfibrinogenemia among patients with chronic thromboembolic pulmonary hypertension

(2009) T. A. Morris et al.   BLOOD

Diagnosis, Pathogenesis, Treatment, and Prognosis of Hereditary Fibrinogen A -Chain Amyloidosis

(2008) J. D. Gillmore et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

QMEAN: A comprehensive scoring function for model quality assessment

(2007) Pascal Benkert et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS