Somtirtha Santra

dblp:439/0346 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2026
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › molecular property prediction
binding affinity prediction
1.012026
BindPred: a framework for predicting protein-protein binding affinity from language model embeddings · Bioinform. 2026
Bioinformatics and computational biology › protein analysis
protein-protein interaction
1.012026
BindPred: a framework for predicting protein-protein binding affinity from language model embeddings · Bioinform. 2026
Bioinformatics and computational biology › protein-protein interaction prediction
sequence-based affinity prediction
1.012026
BindPred: a framework for predicting protein-protein binding affinity from language model embeddings · Bioinform. 2026

Methods — techniques the papers use, named apart from their topics

pyrosetta · 1.0protein language model embeddings · 1.0gradient boosting trees · 1.0bindcraft · 1.0
YearPublicationVenuePosition
2026 BindPred: a framework for predicting protein-protein binding affinity from language model embeddings
abstract
MOTIVATION: Reliable predictions of protein-protein binding affinities are essential for molecular biology and therapeutic discovery. However, most computational methods rely on three-dimensional structural models, which are often unavailable for many complexes. RESULTS: We introduce BindPred, a structure-agnostic input framework that predicts affinities directly from amino acid sequences by combining embeddings from large protein language models with gradient boosting trees. On the protein-protein binding (PPB)-Affinity benchmark, which comprises 11 919 diverse complexes, BindPred achieves a Pearson correlation coefficient of 0.86 in random split five-fold cross-validation. Ablation analysis indicates that evolutionary embeddings alone capture most of the predictive signals, while augmenting with physics-based energy terms from PyRosetta and BindCraft increases the correlation only by 0.01. A more stringent protein-level split that places entire protein families (wild-type and all mutants) exclusively in either training or testing sets, resulting in only a modest decline in performance, demonstrating robust generalization to novel interaction pairs. Because BindPred operates exclusively on sequence input, it enables rapid inference [approximately 3 million complexes per GPU (T4) hour], making proteome-scale screening computationally feasible. AVAILABILITY: The pretrained model and inference pipeline are available in a Google Colab notebook: BindPred Colab notebook. The training dataset, code, and model weights are available on the hugging face: https://huggingface.co/hbp5181/BindPred.
Haixing Piao, Veda Sheersh Boorla, Somtirtha Santra, Costas D. Maranas
Bioinform.3