Leandro de Mattos Pereira (mattoslmp)

mattoslmp

Geek Repo

Company:Computational and System Biologist

Location:Brazil

Home Page:https://mattoslmp.github.io/

Twitter:@mattoslmp

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Leandro de Mattos Pereira's repositories

Annotation-genome-graphics

R scripts for genome annotation graphs

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Microbiota-MetaAnalyser

Microbiota Coral 16S MetaAnalyser

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applied-ml

📚 Papers & tech blogs by companies sharing their work on data science & machine learning in production.

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awesome-AI-based-protein-design

A collection of research papers for AI-based protein design

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BioAutoMATED

Automated machine learning for analyzing, interpreting, and designing biological sequences

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deept2

DeepT2 utilizes deep learning techniques to identify type II polyketide (T2PK) synthases KSβ and their corresponding T2PK product within bacterial genomes. The method leverages ESM2 to transform KSβ sequences into embeddings, which are employed to train two separate classifiers using multi-layer perceptron for both KSβ and T2PKs classification.

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druggpt

DrugGPT: A GPT-based Strategy for Designing Potential Ligands Targeting Specific Proteins

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evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

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exbert

A Visual Analysis Tool to Explore Learned Representations in Transformers Models

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FasterTransformer

Transformer related optimization, including BERT, GPT

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GeneGrouper

CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.

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GPT_protein_design

Efficient protein de novo design pipeline with GPT-based generator and transfer learning-based discrminator

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helm-gpt

HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer

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HGTector

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

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MJPythonNotebooks

Visualizing gene tree conflict using Phyparts, and ETE3

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NeuralPLexer

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

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openai-cookbook

Examples and guides for using the OpenAI API

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papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

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ProstT5

Bilingual Language Model for Protein Sequence and Structure

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protein_scoring

Generating and scoring novel enzyme sequences with a variety of models and metrics

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ProtTrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

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RFdiffusion

Code for running RFdiffusion

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rodeo2

This isn't our first RODEO. The new and improved RODEO is written in Python and supports lasso peptide, class I lanthipeptide, sactipeptide and thiopeptide precursor prediction.

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start-llms

A complete guide to start and improve your LLM skills in 2023 with little background in the field and stay up-to-date with the latest news and state-of-the-art techniques!

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