Protein Secondary Structure Prediction

13 papers with code • 8 benchmarks • 1 datasets

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Datasets


Convolutional ProteinUnetLM competitive with long short-term memory-based protein secondary structure predictors

Kotrix/ProteinUnetLM Proteins 2022

In recent years, a new generation of algorithms for SS prediction based on embeddings from protein language models (pLMs) is emerging.

0
30 Nov 2022

DistilProtBert: A distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts

yarongef/DistilProtBert bioRxiv 2022

Here, we adapted this concept to the problem of protein sequence analysis, by developing DistilProtBert, a distilled version of the successful ProtBert model.

14
10 May 2022
440
10 Feb 2022

DLPAlign: A Deep Learning based Progressive Alignment Method for Multiple Protein Sequences

kuangmeng/DLPAlign 21 Nov 2020

This paper proposed a novel and straightforward approach to improve the accuracy of progressive multiple protein sequence alignment method.

9
21 Nov 2020

ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing

agemagician/ProtTrans 13 Jul 2020

Here, we trained two auto-regressive models (Transformer-XL, XLNet) and four auto-encoder models (BERT, Albert, Electra, T5) on data from UniRef and BFD containing up to 393 billion amino acids.

992
13 Jul 2020

Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction

mircare/Porter5 Scientific Reports 2019

In spite of this, even the most sophisticated ab initio SS predictors are not able to reach the theoretical limit of three-state prediction accuracy (88–90%), while only a few predict more than the 3 traditional Helix, Strand and Coil classes.

43
12 Oct 2019

ProteinNet: a standardized data set for machine learning of protein structure

EricAlcaide/MiniFold 1 Feb 2019

We have created the ProteinNet series of data sets to provide a standardized mechanism for training and assessing data-driven models of protein sequence-structure relationships.

197
01 Feb 2019

High Quality Prediction of Protein Q8 Secondary Structure by Diverse Neural Network Architectures

idrori/cu-ssp 17 Nov 2018

In the spirit of reproducible research we make our data, models and code available, aiming to set a gold standard for purity of training and testing sets.

21
17 Nov 2018

Porter 5: fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes

mircare/Porter5 bioRxiv 2018

Motivation: Although secondary structure predictors have been developed for decades, current ab initio methods have still some way to go to reach their theoretical limits.

43
05 Oct 2018