4.5 Article

AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures

Laszlo Dobson et al.

Summary: AI-driven protein structure prediction, particularly AlphaFold2, has significant implications in the field of structural biology, especially for transmembrane proteins. The TmAlphaFold database provides a valuable tool for accurately assessing protein localization and structure.

NUCLEIC ACIDS RESEARCH (2023)

Article Biochemistry & Molecular Biology

Spatial arrangement of proteins in planar and curved membranes by PPM 3.0

Andrei L. Lomize et al.

Summary: PPM 3.0 is a method and web tool for positioning proteins in curved or planar membranes, particularly those with significant intrinsic curvature in cellular membranes. These proteins are commonly found in mitochondria, plasma membranes, and endosomes.

PROTEIN SCIENCE (2022)

Article Biochemistry & Molecular Biology

Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models

Andrei L. Lomize et al.

Summary: The new version of the Membranome database, Membranome 3.0, has been significantly updated by incorporating models generated by AlphaFold 2. It provides comprehensive structural information on membrane proteins from different organisms and includes new tools for visualization and analysis.

PROTEIN SCIENCE (2022)

Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase in 2021

Alex Bateman et al.

Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

A 10-year meta-analysis of membrane protein structural biology: Detergents, membrane mimetics, and structure determination techniques

Brendon C. Choy et al.

Summary: The study analyzes all uniquely solved membrane protein structures from 2010 to 2019, revealing the significant impact of single-particle cryo-electron microscopy on the field and the unique detergent/membrane mimetic requirements of different structure determination methods and protein classes.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction for the human proteome

Kathryn Tunyasuvunakool et al.

Summary: Using the AlphaFold method, the structural coverage of the proteome has been significantly expanded, covering 98.5% of human proteins with 58% of residues having confident predictions and 36% having very high confidence. Introducing new metrics to interpret the dataset and identify disordered regions, this study aims to provide high-quality predictions for generating biological hypotheses.

NATURE (2021)

Article Biochemistry & Molecular Biology

Critical assessment of methods of protein structure prediction (CASP)-Round XIV

Andriy Kryshtafovych et al.

Summary: CASP is a community experiment aimed at advancing methods for computing three-dimensional protein structure, including rigorous blind testing and evaluation by independent assessors. In the recent CASP14 experiment, deep-learning methods from one research group consistently delivered computed structures rivaling the corresponding experimental ones in accuracy. These results represent a solution to the classical protein-folding problem, at least for single proteins.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2021)

Review Pharmacology & Pharmacy

Membrane protein production and formulation for drug discovery

Ellen Gulezian et al.

Summary: This article reviews the current status and methods of drug discovery using recombinant multipass membrane proteins, which helps overcome challenges in dealing with membrane protein targets and promotes the development of highly specific therapies.

TRENDS IN PHARMACOLOGICAL SCIENCES (2021)

Article Biology

Structure and analysis of nanobody binding to the human ASIC1a ion channel

Yangyu Wu et al.

Summary: The study demonstrates that nanobodies derived from alpacas specifically target human ASIC1a, offering potential therapeutic applications in modulating pain, fear, addiction, and ischemia-induced neuronal injury. In addition, the nanobody Nb.C1 can enhance inhibitory effects of tarantula toxin PcTx1 on hASIC1a and serve as a molecular tool for biochemical and structural studies of hASIC1a.
Review Biochemistry & Molecular Biology

Highlighting membrane protein structure and function: A celebration of the Protein Data Bank

Fei Li et al.

Summary: Biological membranes define cell boundaries and compartmentalize processes, with the study of membrane protein structures playing a vital role in understanding their biological functions. Deposition of membrane protein structures into the PDB since 1985 allows for deeper insights, magnifying their impact in biology. Free access to membrane protein structures facilitates broader understanding and crucial new insights into their biological functions.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

Article Biochemistry & Molecular Biology

Cryo-EM structure of the entire mammalian F-type ATP synthase

Gergely Pinke et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

Article Biochemistry & Molecular Biology

The PSIPRED Protein Analysis Workbench: 20 years on

Daniel W. A. Buchan et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions

Thomas D. Newport et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

Balint Meszaros et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Membrane protein structural biology in the era of single particle cryo-EM

Yifan Cheng

CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)

Article Chemistry, Medicinal

Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures

Jack Hanson et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)

Article Chemistry, Multidisciplinary

Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning

Rhys Heffernan et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2018)

Article Multidisciplinary Sciences

The in silico human surfaceome

Damaris Bausch-Fluck et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Biochemical Research Methods

Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers

Andrei L. Lomize et al.

BIOINFORMATICS (2018)

Article Biology

The human transmembrane proteome

Laszlo Dobson et al.

BIOLOGY DIRECT (2015)

Review Biochemistry & Molecular Biology

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Zoe Cournia et al.

JOURNAL OF MEMBRANE BIOLOGY (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

Daniel Kozma et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

OPM database and PPM web server: resources for positioning of proteins in membranes

Mikhail A. Lomize et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemical Research Methods

Prediction of the human membrane proteome

Linn Fagerberg et al.

PROTEOMICS (2010)

Review Pharmacology & Pharmacy

Computational analysis of membrane proteins: the largest class of drug targets

Yalini Arinaminpathy et al.

DRUG DISCOVERY TODAY (2009)

Article Multidisciplinary Sciences

Biophysical dissection of membrane proteins

Stephen H. White

NATURE (2009)

Article Biochemistry & Molecular Biology

Biochemical and genetic studies of UBR3, a ubiquitin ligase with a function in olfactory and other sensory systems

Takafumi Tasaki et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2007)

Article Biochemical Research Methods

TMDET:: web server for detecting transmembrane regions of proteins by using their 3D coordinates

GE Tusnády et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

AL2CO: calculation of positional conservation in a protein sequence alignment

JM Pei et al.

BIOINFORMATICS (2001)